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

Science Focus Area: Lawrence Berkeley National Laboratory

  • Principal Investigator: Trent R. Northen1
  • Technical Co-Manager: Adam M. Deutschbauer1
  • Co-Investigators: Jillian F. Banfield2, Rodolphe Barrangou3, Romy Chakraborty1, Jennifer A. Doudna2, N. Louise Glass2, Jenny C. Mortimer1,6, Aindrila Mukhopadhyay1, Daniel Segrè4, Anup K. Singh5, John Vogel1, Kateryna Zhalnina1
  • Participating Institutions: 1Lawrence Berkeley National Laboratory, 2University of California at Berkeley, 3North Carolina State University, 4Boston University, 5Lawrence Livermore National Laboratory, 6University of Adelaide
  • Project Website: mcafes.lbl.gov
  • Related Website: fabricatedecosystems.lbl.gov
mCafes diagram

m-CAFES. The m-CAFEs SFA, led by Lawrence Berkeley National Laboratory (LBNL), is developing and deploying unique laboratory capabilities that capture key aspects of grass rhizosphere communities in the field and identify the causal mechanisms that govern microbial interactions within the rhizosphere. Computational modeling is used to predict interactions and responses that are then tested experimentally and refined until they accurately predict field processes. [Courtesy LBNL]

Summary

The Microbial Community Analysis and Functional Evaluation in Soils (m-CAFEs) project is a multi-institutional Science Focus Area (SFA) aimed at understanding the interactions, localization, and dynamics of grass rhizosphere communities at the molecular level (i.e., genes, proteins, metabolites). Gaining this understanding will enable prediction of community responses to perturbations and insights into the persistence and fate of engineered genes and microbes for secure biosystems design. To achieve this understanding, advanced fabricated ecosystems (called EcoFABs) are used in combination with gene-editing technologies such as CRISPR-Cas and bacterial-virus approaches (i.e., phage-based methods) to interrogate gene and microbial functions in situ—addressing key challenges highlighted in recent U.S. Department of Energy reports. This work is integrated with the development of predictive computational models that are iteratively refined through simulation and experimentation. Simplified microbial consortia assembled in the laboratory are used in combination with studies of partially reduced, native soil-derived microbial communities to gain critical insights into engineered genes and microbes within soil microbiomes and the biology and ecology of uncultivated microbes. This SFA is currently piloting meter-scale contained and controlled ecosystems (called EcoPODs) that enable the extension of m-CAFEs science into more complex environments. The research on microbial communities leverages the team’s extensive expertise in CRISPR-Cas systems, phage biology, genome-resolved metagenomics, high-throughput bacterial and fungal genetics, and systems biology, as well as plant mutant collections and phenotyping capabilities. Together, these efforts lay a critical foundation for developing secure biosystems design strategies, harnessing beneficial microbiomes to support sustainable bioenergy, and improving the understanding of nutrient cycling in the rhizosphere. The knowledge gained and approaches pioneered by m-CAFEs can be extended to other ecosystems and will advance microbiome research toward a more predictive and causative science.

2024 Abstracts

TitlePIPI InstitutionPresenter
Understanding Plant/Environmental Interactions Using Single-Cell ApproachesColeDOE Joint Genome InstituteColeEarly Career
Using Cell-Free Systems to Accelerate Biosystems Design for Carbon-Negative ManufacturingJewettNorthwestern UniversityChoi and ZolkinUniversity
Converting Methoxy Groups on Lignin-Derived Aromatics from a Toxic Hurdle to a Useful Resource: A Systems-Driven ApproachMarxUniversity of IdahoAllemanUniversity
Mapping Enzymatic Esterification to Natural Expression Levels for a Specialized Clade of HCT Acyltransferases in PoplarFoxGreat Lakes Bioenergy Research CenterFoxGLBRC
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in CyanobacteriaYoungVanderbilt UniversityZunigaUniversity
Utilizing Cryo-Electron Microscopy to Characterize Proteins Relevant to Biomass Biosynthesis and BioconversionTuskanCBIZieglerCBI
Investigating Cellular Network and Outer-Membrane Vesicles for the Metabolism of Lignin-Derived Aromatics in Soil Pseudomonas SpeciesAristildeNorthwestern UniversityZhouUniversity
Metabolomics Investigates the Impact of Plastic Biodegradation on Mealworm Gut MicrobiomeBlennerUniversity of DelawareZhaoUniversity
Transformations of Soil Organic Carbon Influenced by Volatile Organic CompoundsMeredithUniversity of ArizonaLunnyUniversity
Using Finlay-Wilkinson Regression to Analyze Genotype–Environment Interaction for Biomass from Switchgrass Field TrialsJuengerUniversity of Texas–AustinZhangUniversity
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood DecomposerZhangUniversity of Minnesota–Saint PaulSchillingUniversity
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and ConversionO’MalleyUniversity of California–Santa BarbaraZhangUniversity
Characterizing Bacterial–Fungal Interactions Within Soil Niches and Across Soil MineralogiesNguyenUniversity of Hawai'i–MānoaZebaUniversity
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene SynthesisNorthThe Ohio State UniversityYoungUniversity
Population Genomic Differentiation of the Ectomycorrhizal Fungus Suillus pungens Along a Climate GradientPeayStanford UniversityYeamUniversity
Phenotypic and Molecular Characterization of Nitrogen-Responsive Genes in SorghumYangUniversity of Nebraska–LincolnYangUniversity
Quantitative Plant Science Initiative: Integrating Functional Genomics with Biomolecular-Level Experimentation to Understand Adaptation to Micronutrient Stress in Poplar and SorghumLiuBrookhaven National LaboratoryXieQPSI
Mapping Perturbations in a Naturally Evolved Fungal Garden Microbial ConsortiumBurnum-JohnsonPacific Northwest National LaboratoryWuEarly Career
Systems-Level Insights into the Physiology of Methane-Fueled Syntrophy Between Anaerobic Methanotrophic Archaea and Sulfate-Reducing BacteriaOrphanCalifornia Institute of TechnologyMayrUniversity
Renewed Utility of Tyrosine IntegrasesSchoenigerSandia National LaboratoriesWilliamsInCoGenTEC 
Optimizing Biological Funneling of Lignin Streams by Comparison in Several Microbial PlatformsTuskanCBIWilkesCBI
Plant-Microbe Interfaces: Disentangling Microbial-Mediated Plant Stress Tolerance with Synthetic Communities and Automated PhenotypingDoktyczOak Ridge National LaboratoryWestonPlant-Microbe Interfaces
Prototyping Carbon-Conserving Networks for Diacid ProductionCarothersUniversity of WashingtonWestenbergUniversity
Molecular and Cellular Responses of Human Endothelial Cells to Low-Dose RadiationStevensArgonne National LaboratoryWeinbergLow-Dose
Beneficial Plant-Fungal Partnerships in the Resource Economy of Bioenergy GrassesStuartLawrence Livermore National LaboratoryNuccioµBiospheres
Integrated Experimental Approaches to Understand Bioenergy Crop Productivity Through Rhizosphere ProcessesZenglerUniversity of California–San DiegoNorthenUniversity
Amphiphilic Cosolvents Disrupt the Lateral Structure of Model Biomembranes and Reveal an Unrecognized Mode of Cell Stress DavisonOak Ridge National LaboratoryNickelsBiomass Deconstruction
Reactive Transport Modeling for Prediction of Nitrous Oxide Emission from the Subsurface Observatory at a Nitrate-Contaminated Site in Response to Rainfall EventsAdamsLawrence Berkeley National LaboratoryNewcomerENIGMA
Metabolic Remodeling: Stylish Options for Bacterial Interior DesignNeidleUniversity of Georgia–Athens NeidleUniversity
Engineering a Carbon Dioxide Concentrating Mechanism in Cupriavidus necator for Carbon-Negative BiomanufacturingJewettStanford University–Palo AltoNakamuraUniversity
Enabling Synthetic Biology in Setaria and Sorghum Through Targeted Mutagenesis and Programmed Transcriptional RegulationBaxterDonald Danforth Plant Science CenterMyersUniversity
The Enigma of N2 Fixation in Energy-Limited Anaerobic Methane-Oxidizing Microbial ConsortiaOrphanCalifornia Institute of Technology–PasadenaMuraliUniversity
Engineering Auxenochlorella protothecoides: Artificial Chromosomes, Regulators of Lipid Biosynthesis, and Improving PhotosynthesisMerchantUniversity of California–BerkeleyMoseleyUniversity
Transgenic Perturbation of Winter-Biased Genes in PopulusTsaiUniversity of Georgia–AthensMoradPourUniversity
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood TraitsShabekUniversity of California–DavisMoe-LangeUniversity
Understanding the Molecular Rules of Transporter Specificity to Engineer Biofuel-Relevant Efflux PumpsDonohueUniversity of Wisconsin–MadisonMillerGLBRC
Systems Metabolic Engineering of Novosphingobium aromaticivorans for Lignin ValorizationMichenerOak Ridge National LaboratoryMichenerEarly Career
The Plant Synthetic Biology Shared Research Objective: Building a Cross-BRC Repository of Regulatory Elements and Testing TechnologiesDonohueUniversity of Wisconsin–MadisonMcKay WhitemanGLBRC
Model Communities of Soil Microbiomes Reveal Details of Carbon-Use Efficiencies and Interkingdom Interactions Across ScalesHofmockelPacific Northwest National LaboratoryMcClurePhenotypic Response of SOIL Microbes
Mechanisms and Flux Measurements of Microbial Processing of Photosynthetically Fixed Algal Carbon Using Isotope Tracing and Secondary Ion Mass SpectrometryStuartLawrence Livermore National LaboratoryMayaliµBiospheres
Flow Sorting and Sequencing Active Environmental Viruses from Methane-Oxidizing Communities with Viral-BONCATOrphanCalifornia Institute of Technology–PasadenaMartinez-HernandezUniversity
Evolutionary Flexibility and Rigidity in the Bacterial Methylerythritol Phosphate PathwayDonohueUniversity of Wisconsin–MadisonMarshallGLBRC
Discovery and Functional Characterization of Genomic Islands for Non-model Bacterial SystemsSchoenigerSandia National LaboratoriesMageeneyInCoGenTEC 
Single-Cell and Spatial Regulatory Map of PoplarBuellUniversity of GeorgiaLuoUniversity
The Complex System of Organic Carbon Remineralization in Rapidly Thawing Svalbard Permafrost and Active Layer SoilsLloydUniversity of TennesseeLloydUniversity
A Prompt Engineering Approach for Root Confocal Image Segmentation Using the Segment Anything ModelDinnenyStanford University–Palo AltoLiUniversity
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-Fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform ChemicalsLinUniversity of Michigan–Ann ArborLinUniversity
Systems-Level Analysis of Extreme Differences in Fatty Acid Chain-Length Production: Natural Variants and Redesigned Brassicaceae OilseedsCahoonUniversity of Nebraska–LincolnLingwanUniversity
Principles Governing Expression of Overlapping GenesJiaoLawrence Livermore National LaboratoryLimMicrobial Secure Biosystems Design
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome OptimizationJewettNorthwestern University–EvanstonLiewUniversity
Massive Protein Redesign to Make Overlapping GenesJiaoLawrence Livermore National LaboratoryLeonardMicrobial Secure Biosystems Design
Advancing Towards Synthetic Biology that Can Detect and Control Plant-Fungal InteractionsAbrahamOak Ridge National LaboratoryLeBoldusSEED
Quantitative Trait Locus Mapping of Swarming Motility and Germination Rate in a Bacillus subtilis LibraryTuskanCBILagergrenCBI
Unraveling Metabolic Interactions Within a Rhizosphere Microbial CommunityZenglerUniversity of California–San DiegoKumarUniversity
Influence of Temperature on Arctic Lake Sediment Methane Production and Organic Matter CompositionVarnerUniversity of New HampshireKuhnUniversity
Natural Diversity Screening, Assay Development, and Characterization of Nylon-6 Enzymatic DepolymerizationKucharzykBattelle Memorial InstituteBeckhamUniversity
Study of the 4-Hydroxybenzoate Catabolic Pathway in White-Rot Fungi via Biochemical and Structural Enzyme CharacterizationSalvachúaNational Renewable Energy LaboratoryKuatsjahEarly Career
Strengthening Educational and Research Capacity for Bioenergy Science at Alabama A & M University through a Combination of Education, Research, and PartnershipsCebertAlabama A & M University–NormalKuangRENEW
Harnessing Bacterial-Fungal Interactions to Improve Switchgrass Nitrogen-Use EfficiencyEvansMichigan State UniversityKristyUniversity
Microbial Networks Demonstrate Extraordinary Metabolic Versatility and the Ability to Obtain Electron Acceptors from Soil Organic Matter in Temperate Peatland SoilsKostkaGeorgia Institute of Technology–AtlantaKostkaUniversity
Root Biosynthesis Engineering of the “Plant Diamond” Sporopollenin for Permanent Belowground Carbon StorageKirstUniversity of Florida–GainesvilleKirstEnergy Earthshots
Charting the Path to Optimize Polysaccharide Accumulation in Bioenergy SorghumDonohueUniversity of Wisconsin–MadisonKimGLBRC
Achieving High Productivity of 2-Pyrone-4,6-dicarboxylic acid (PDC) from Aqueous Aromatic Streams with Novosphingobium aromaticivoransDonohueUniversity of Wisconsin–MadisonKimGLBRC
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic FeedstocksSolomanUniversity of Delaware–Newark; Purdue University–West LafayetteKhimUniversity
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction, and Function in KnowledgebasePett-RidgeLawrence Livermore National LaboratoryMarschmannMicrobes Persist SFA
Intraspecific Genetic Variation in Populus trichocarpa Influences Above and Belowground Plant Chemistry and Influences Plant-Soil InteractionsTuskanCBIKalluriCBI
Response of Methanotroph Communities to Warming Temperatures in a Recently Thawed FenVarnerUniversity of New Hampshire–DurhamJonesUniversity
Field Observation of Water, Sediment, and Nutrient Distribution Patterns in Alluvial Ridge Basins Between the Abandoned Rio Grande Channels (Resacas)DongUniversity of Texas Rio Grande ValleyDongFAIR
Knocking Out a Candidate Gene for Wax Production in Switchgrass Results in an Unexpected Pleiotropic PhenotypeTuskanCBIDevosCBI
BER-RENEW iSAVe: New Energy Sciences Workforce to Advance Innovations in Sustainable Arid VegetationKalyuzhnayaSan Diego State UniversityDelherbeRENEW
Synthetic Biology Tools to Reliably Establish and Monitor Microbial Invasions in the RhizosphereAbrahamOak Ridge National LaboratoryDel Valle KessraSEED
ENIGMA Environmental Simulations and Modeling: Predictive Modeling and Mechanistic Understanding of Field ObservationsAdamsLawrence Berkeley National Laboratoryde RaadENIGMA
Improving Bioprocess Robustness by Cellular Noise EngineeringStephanopoulosMassachusetts Institute of TechnologyDaletosUniversity
Probing the Mechanisms of Microbial Mediated Polymer Deconstruction on the Molecular- and Systems-LevelRodriguezUCLA-DOE InstituteClubUniversity
EndoPopulus: Endophyte Inoculation Alters Whole-Plant Physiology and Growth Dynamics of Populus Under Nitrogen-Deficient ConditionDotyUniversity of Washington–SeattleChungUniversity
How Soils WorkPett-RidgeLawrence Livermore National LaboratoryChuckranMicrobes Persist SFA
Developing Reduced Complexity Microbial Communities for Editing Across ScalesNorthenLawrence Berkeley National LaboratoryChiniquym-CAFEs
Stopping Escape and Malfunction in Genetic Code Engineered CellsChurchHarvard UniversityChiappino-PepeUniversity
Connecting Microbial Genotype to Phenotype in Bacterial Strains from a Dynamic Subsurface Ecosystem Using ENIGMA 'Environmental Atlas'AdamsLawrence Berkeley National LaboratoryChakrabortyENIGMA
Modulating Bioenergy Traits in Field-Grown Sorghum Affects the Rhizosphere Bacterial CommunitiesKeaslingJBEIChaiJBEI
The Fungal Microbiome: Discovering and Investigating Novel Endohyphal InhabitantsChainLos Alamos National LaboratoryChainBacterial-Fungal Interactions
Automation of a CRISPRi Platform for Enhanced Isoprenol Production in Pseudomonas putidaKeaslingJBEICarruthersJBEI
Plant-Microbe Interfaces: Microbially Mediated Host Stress Response—Bridging Field and Laboratory Experiments to Gain Insights into the Populus-Microbiome Symbiosis Under Abiotic StressDoktyczOak Ridge National LaboratoryCarrellPlant-Microbe Interfaces
Towards a Mechanistic Understanding of Rhodanobacter Dominance in the Contaminated SubsurfaceAdamsLawrence Berkeley National LaboratoryCarlsonENIGMA
Knowledge-Guided Interrogation of the Plastid Fatty Acid BiofactoryCahoonUniversity of Nebraska–LincolnJorgeUniversity
Development of High-Throughput Methods to Assist Measure of Biological Nitrification Inhibition in Populus SoilsCahillOak Ridge National LaboratoryCahillEarly Career
Metabolic Engineering of Issatchenkia orientalis for Cost-Effective Production of CitramalateLeakeyCABBIBunCABBI
BioPoplar: A Tunable Chassis for Diversified Bioproduct ProductionRobin BuellUniversity of Georgia–AthensRobin BuellUniversity
Lipid Membrane Biology of Microbial Cell Factories During Microaerobic FermentationBudinUniversity of California–San DiegoBudinEarly Career
Engineering Continuous Trait Variation in Bioenergy Feedstocks to Optimize Growth on Marginal LandsBrophyStanford UniversityBrophyEarly Career
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve ProductivityLeonelliUniversity of Illinois Urbana-ChampaignBrooksUniversity
Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon CyclingNuccioLawrence Livermore National LaboratoryBrissonEarly Career
Assessing the Effect of Nitrogen and Phosphorus Fertilization on Root-Microbial Communities and Yield Response in Sorghum bicolorBennetzenUniversity of Georgia–AthensBrailey-JonesUniversity
A Systems Approach for Predicting Metabolic Fluxes in Auxenochlorella protothecoidesMerchantUniversity of California–BerkeleyBoyleUniversity
Rendering the Metabolic Wiring Powering Wetland Soil Methane ProductionWrightonColorado State University–Fort CollinsBortonUniversity
Unraveling Microbial and Viral Responses to Wetting Using MultiomicsPett-RidgeLawrence Livermore National LaboratoryBlazewiczMicrobes Persist SFA
Climate vs. Energy Security: Quantifying the Trade-Offs of BECCS Deployment and Overcoming Opportunity Costs on Set-Aside LandLeakeyCABBIBlanc-BetesCABBI
Beyond Boundaries: Foxtail Mosaic Virus Drives Heterologous Protein Expression and Precision Gene Editing in SorghumLeakeyCABBIBaysalCABBI
Characterizing Mechanistic Roles of Viruses in Driving Biogeochemical Cycles in the RhizosphereMounceyLawrence Berkeley National LaboratoryBassonJGI
Performance Thresholds for Co-Utilization of Lignin-Derived Aromatics and SugarsKeaslingJBEIBaralJBEI
Response of Soil Microbial Communities to Nitrogen and Phosphorus Input in Sorghum FieldBennetzenUniversity of Georgia–AthensBabalolaUniversity
The Lawrence Livermore National Laboratory Cryo-NanoSIMS: The Next Generation for High Spatial Resolution Functional AnalysisStuartLawrence Livermore National LaboratoryWeberµBiospheres
Applying Metabolic Models to Mechanistically Understand and Predict Interactions Between Anaerobic Methanotrophic Archaea and Sulfate-Reducing Bacteria Strains in Geochemical Cycling ProcessesHenryArgonne National LaboratoryLiuUniversity
Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native EcosystemsGuarnieriNational Renewable Energy LaboratoryArnoldsIMAGINE BioSecurity
Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis ApplicationsYungLawrence Livermore National LaboratoryWackelinEarly Career
Identification of the Genetic Factors that Contribute to Biological Nitrogen Fixation in Sorghum (Sorghum bicolor)AneUniversity of Wisconsin–MadisonVenadoUniversity
Drought-Induced Plant Physiology Drives Altered Microbe-Metabolite Interactions Along the Plant Rhizosphere ColumnEgbertPacific Northwest National LaboratoryAnthonyPersistence Control of Soil Microbiomes
Enhancing Biological Nitrogen Fixation in Sorghum (Sorghum bicolor) Aerial Roots Through Engineering Diazotrophic CommunitiesAneUniversity of Wisconsin–MadisonVenadoUniversity
Vision-Driven RhizoNet: Foundations for Systematic Measurement of Plant Root BiomassTringeLawrence Berkeley National LaboratoryUshizimaEERC
How Microbes and Minerals Make Necromass that PersistsDeAngelisUniversity of Massachusetts–AmherstAndersonUniversity
Functional Characterization of GT47 Glycosyltransferases in Duckweed to Facilitate Predictive BiologyUrbanowiczUniversity of GeorgiaUrbanowiczUniversity
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic RubberTullman-ErcekNorthwester UniversityTullman-ErcekUniversity
Exploring the Metabolic Capability of Undomesticated Thermophilic Bacillus coagulans for Biosynthesis of Designer Esters at Elevated TemperaturesTrinhUniversity of Tennessee–KnoxvilleTrinhUniversity
Multiscale Computational Digital Twins for Whole-Body to Subcellular Radiation EffectsStevensArgonne National LaboratoryAgasthyaLow-Dose
RESTOR-C: Center for Restoration of Soil Carbon by Precision Biological StrategiesTringeLawrence Berkeley National LaboratoryTringeEERC
High (School) Throughput Screening of BAHD TransferasesAchesonUniversity of Wisconsin–MadisonAchesonGLBRC
Understanding the Role of Permafrost-Affected Microbes in Thawing ArcticLloydUniversity of Tennessee–KnoxvilleAbuahUniversity
Understanding Microbial Invasion Biology from Laboratory-to-Field for Secure Ecosystem Engineering and DesignAbrahamOak Ridge National LaboratoryAbrahamSEED
Progress Towards the Generation of Oily MiscanthusLeakeyUniversity of Illinois Urbana–ChampaignTrieuCABBI
Developing Temperature-Jump X-Ray Crystallography to Study Dynamic Biosynthetic Enzymes at Synchrotrons and X-Ray Free-Electron LasersThompsonUniversity of California–MercedThompsonFAIR
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel ProductionZenglerUniversity of California–San DiegoThiruppathyUniversity
CRISPR Activation of Poplar Target of Rapamycin Genes Improves Nitrogen Use Efficiency and Indicates Possible Functional DivergenceColemanUniversity of MarylandTayengwaUniversity
From Viromes to Virocells: Dissecting Viral Roles in Terrestrial Microbiomes and Nutrient CyclingSullivanThe Ohio State UniversitySullivanUniversity
Iron-Mediated Microbial Interactions with Primary Producers in Terrestrial and Aquatic SystemsStuartLawrence Livermore National LaboratoryStuartµBiospheres
AI Foundation Models for Understanding Cellular Responses to Radiation ExposureStevensArgonne National LaboratoryStrokaLow-Dose
Cryosectioning-Enabled Super-Resolution Microscopy for Studying Nuclear Architecture at the Single Protein LevelChurchHarvard Medical SchoolSteinUniversity
Understanding the Role of Tolerance on Microbial Production of IsoprenolKeaslingJBEISrinivasanJBEI
Leveraging Type I-F CRISPR-Associated Transposase Regulators to Improve Editing EfficiencyNorthenLawrence Berkeley National LaboratorySongm-CAFEs
Interactions Between Enhanced Rock Weathering and Soil Organic Carbon Cycling in Coordinated, National-Scale Field TrialsPett-RidgeLawrence Livermore National LaboratorySokolEERC
Synthetic Biology Tool Development for Precision Engineering of Oilseed CropsCahoonUniversity of Nebraska–LincolnSmanskiUniversity
Multiomics-Driven Microbial Model OptimizationCarothersUniversity of Washington–SeattleShinUniversity
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil CarbonMeredithLawrence Berkeley National LaboratoryShenUniversity
Microbial Treatments to Increase Carbon Sequestration in Biofuel Crop SystemsTringeLawrence Berkeley National LaboratorySevanto
Global Proteomics and Resource Allocation Modeling Reveals Thermodynamic Bottleneck and Highlights Effective Genetic and Metabolic Interventions for C. thermocellumTuskanCBISchroederCBI
Leveraging Leaf Structure and Biochemistry to Enhance Water Use Efficiency in SorghumBaxterDonald Danforth Plant Science CenterSchraderUniversity
Computational Modeling to Enable Predictive Secure Biosystems DesignsGuarnieriNational Renewable Energy LaboratorySantibanez PalominosIMAGINE BioSecurity
Understanding the Role of Duckweed Transcription Factor in Triacylglycerol Metabolism and Abiotic Stress Tolerance in PlantsMuthanWest Virginia State UniversitySanjayaFAIR
Designing Novel Enzymes for Complete Degradation of Recalcitrant PolyamidesZanghelliniArzeda CorporationSangha
Real-Time Sensing and Adaptive Computing to Elucidate Microenvironment-Induced Cell Heterogeneities and Accelerate Scalable BioprocessesSalvachúaNational Renewable Energy LaboratorySalvachúaAccelerate
Extracting Switchgrass Features Through Minirhizotron and Hyperspectral Image ProcessingJuengerUniversity of Texas–AustinSaldanhaUniversity
Plant-Microbe Interfaces: Specialized Fungal Metabolites Regulate Synthetic Fungal Communities and Their Interactions with PopulusDoktyczOak Ridge National LaboratoryRushPlant-Microbe Interfaces
Multiomics Pipelines and Approaches to Characterize Viral Impacts on Environmental MicrobiomesRouxDOE Joint Genome InstituteRouxEarly Career
Mapping Toxin-Antitoxin Systems for Microbial Community BiocontainmentJiaoLawrence Livermore National LaboratoryRicciMicrobial Secure Biosystems Design
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping DatasetsRellán-ÁlvarezNorth Carolina State UniversityRellán-ÁlvarezUniversity
Microbial Responses to Scaling Complexity in Chitin Decomposition with Changing Moisture and Structure LevelsHofmockelPacific Northwest National LaboratoryReichartPhenotypic Response of SOIL Microbes
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic StressCreggerOak Ridge National LaboratoryRamírez-FloresEarly Career
Using Biodiversity to Explore the Diversification of Environment-Regulated GrowthDinnenyStanford UniversityRamachandranUniversity
Structural Characterization of GT47 Glycosyltransferases in Duckweed to Facilitate Predictive BiologyUrbanowiczNational Renewable Energy LaboratoryPrabhakarUniversity
Transcriptional Profiling of Winter-Regulated Genes in Populus trichocarpaTsaiUniversity of GeorgiaPloyetUniversity
Characterization, Neutron Scattering, and Molecular Dynamic Simulation of the Lignin Carbohydrate Complex Structure and its DisruptionDavisonUniversity of Tennessee–KnoxvilleVenkatesh PingaliBiomass Deconstruction
Terraforming Soil Energy Earthshot Research Center: Accelerating Soil-Based Carbon Drawdown Through Advanced Genomics and GeochemistryPett-RidgeLawrence Livermore National LaboratoryPett-RidgeEERC
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical ProductionPeterUniversity of FloridaPeterUniversity
Plant-Microbe Interfaces: Defining Quorum Sensing Signal Potential in the Populus Microbiome and Examining its Role in Community Selection and StructureDoktyczOak Ridge National LaboratoryPelletierPlant-Microbe Interfaces
The Root Microbiome of Camelina: From Structure to FunctionLuMontana State UniversityPaulitzUniversity
Friends and Foes: How Microbial Predators Influence Nutrient Cycling in SoilHungateNorthern Arizona UniversityPatelUniversity
Deciphering Stress-Resilient Growth in Brassicaceae Models: A Comparative Genomics Analysis of Adaptative on to Extreme EnvironmentsDinnenyStanford UniversityPanthaUniversity
Unleashing Photosynthesis and Nitrogen Fixation for Carbon Neutral Production of Nitrogen-Rich CompoundsPakrasiWashington University in St. LouisPakrasiEnergy Earthshots
Conversion of Lignocellulosic Plant Biomass into Industrial Chemicals via Metabolic Engineering of Two Extreme Thermophiles, Caldicellulosiruptor bescii and Pyrococcus furiosusAdamsUniversity of GeorgiaO'QuinnUniversity
Developing Chassis for Low Density Polyethylene Upcycling from Microbes Native to the Gut Microbiome of Yellow MealwormsBlennerUniversity of DelawareOttUniversity
Cell-Free Systems Biology: Characterizing Pyruvate Metabolism of Clostridium thermocellum with a Three-Enzyme Cascade ReactionOlsonDartmouth CollegeOlsonUniversity
Bacterial Degradation of Sorgoleone, a Step Towards Enforcing Rhizobacteria ContainmentEgbertPacific Northwest National LaboratoryOdaPersistence Control of Soil Microbiomes
Construction of a Synthetic 57-Codon E. coli Chromosome to Achieve Resistance to All Natural Viruses, Prevent Horizontal Gene Transfer, and Enable BiocontainmentChurchHarvard Medical SchoolNyergesUniversity
Assessing Bacterial-Fungal Interactions Across Experimental ScalesChainLos Alamos National LaboratoryJohnsonBacterial-Fungal Interactions
Sequencing Driven Accelerated Discovery of Genes Regulating Water Use Efficiency and Stomatal Patterning and in C4 Crops with High-Throughput PhenotypingBaxterDonald Danforth Plant Science CenterJiangUniversity
Reduced Environmental Plasticity in Pennycress Improves Responses to Competition and Climate ChangeSedbrookIllinois State UniversityJawahirUniversity
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic PathwaysJarboeIowa State UniversityJarboeUniversity
Multichromatic Optogenetic Control of Microbial Co-Culture Populations for Chemical ProductionAvalosPrinceton UniversityJangUniversity
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum BiomassKirstUniversity of FloridaPereiraUniversity
Conversion of Natural and Transgenic Sugarcane and Poplar Variants with an Ionic-Liquid-Based Feedstocks-To-Fuels PipelineKeaslingJBEIIslamJBEI
Engineering Inducible Biological Nitrogen Fixation for Bioenergy CropsDonohueDOE Great Lakes Bioenergy Research CenterInfanteGLBRC
Role of Nitrogen Oxides in a High Nitrate and Heavy Metal Contaminated Field Site: What Has Been Observed and What Researchers Aim to UnderstandAdamsLawrence Berkeley National LaboratoryHuntENIGMA
Machine Learning-Assisted Genome-Wide Association Study Uncovers Copy-Number Variations of Tandem Paralogs Driving Stress Tolerance Evolution in Issatchenckia orientalisLeakeyDOE Center for Bioenergy and Bioproducts InnovationHsiehCABBI
Comparison of Soil Responses to Long-Term Fertilization and Short-Term Nitrogen and Carbon Amendments in Miscanthus and CornLeakeyDOE Center for Advanced Bioenergy and Bioproducts InnovationHoweCABBI
Drought Influences Microbial Activity and the Accrual and Composition of Soil Organic CarbonPett-RidgeLawrence Livermore National LaboratoryHoneckerMicrobes Persist SFA
Profiling Temporal and Spatial Activities of RhizobacteriaAdamsDOE Joint Genome InstituteHondaJGI
Metabo-Lipidomics Unveil Root Exudate Molecular Diversity and Functional Impacts on Soil Microbial CommunitiesHofmockelPacific Northwest National LaboratoryHofmockelPhenotypic Response of SOIL Microbes
Legacy Effects of Warming Alter Simple and Complex Soil Organic Matter DecompositionHungateNorthern Arizona UniversityHoffmanUniversity
Plant-Microbe Interfaces: Unraveling How Microbial Adaptation Strategies Are Shaped by the Chemical Environment of the Populus RhizosphereDoktyczOak Ridge National LaboratoryHettichPlant-Microbe Interfaces
Dissecting Bacterial-Fungal Interactions in the Bouteloua gracilis Rhizosphere Microbiome Using Metabolic PhenotypingChainLos Alamos National LaboratoryHansonBacterial-Fungal Interactions
Plastic Degradation and Upcycling by the Gut Microbiome of Yellow MealwormsSolomonUniversity of DelawareHansenUniversity
CRISPR/Cas Tool Development and Genome Engineering in Nonmodel BacteriaCarothersUniversity of WashingtonGuzmanUniversity
EcoFAB 3.0: A Controlled Ecosystem for Bioenergy CropsKeaslingJBEIGuptaJBEI
IMAGINE BioSecurity: Genome-Scale Engineering and High-Throughput Screening to Establish Secure Biosystems DesignGuarnieriNational Renewable Energy LaboratoryGuarnieriIMAGINE BioSecurity
Physical and Molecular Responses of Pennycress (Thlaspi arvense L.) to Waterlogging SedbrookIllinois State UniversityGschwendUniversity
Analyzing Biotic and Abiotic Stress Responses in Sorghum Using Comprehensive Field Phenomics DataEvelandDonald Danforth Plant Science CenterGonzalezUniversity
Pyrocosms to Measure Influence of Fire Intensity, Time, and Soil Depth on Microbial Succession, Cross-Kingdom Interactions, and Greenhouse Gas EmissionsGlassmanUniversity of California–RiversideGlassmanUniversity
Optimizing Enzymes for Plastic Upcycling Using Machine Learning Design and High Throughput ExperimentsGauthierHarvard Medical SchoolGauthierUniversity
Engineering Cupriavidus necator for Efficient Aerobic Conversion of Carbon Dioxide (CO2) to Fuels and ChemicalsJewettStanford UniversityFulkUniversity
Engineering C4 Feedstock Crops for Improved Water Use Efficiency and Drought AvoidanceBaxterDonald Danforth Plant Science CenterFischerUniversity
Integrating Molecular Genetics and Precision Phenotyping to Elucidate the Genetic Basis for Drought Resilience in SorghumEvelandDonald Danforth Plant Science CenterEvelandUniversity
Dead or (Still Not) Alive: Patterns and Drivers of Soil Viral Activity, Turnover, and DecayEmersonUniversity of California–DavisEmersonUniversity
Reinforced CRISPR Interference (CRISPRi) Enables Reliable Multiplex Gene Repression In Phylogenetically Distant BacteriaEgbertPacific Northwest National LaboratoryElmorePersistence Control of Soil Microbiomes
Surveying, Culturing, and Sequencing Root Microbiomes Associated with Switchgrass, a Native North American Biofuel FeedstockJuengerUniversity of Texas–AustinEdwardsUniversity
Unveiling Molecular Interactions and Metabolic Contributions in Sorghum Anthracnose Defense: Towards the Integration of Fungal Pathogen and Host Sorghum ModelsLiuBrookhaven National LaboratoryEdirisingheBRaVE
Systems Framework to Enhance the Potential of Camelina as Oilseed CropGrotewoldMichigan State UniversityEdgerUniversity
Thermophilic Genetic Tool Development for Engineering and Functional Genomics in Clostridium thermocellumTuskanCBIEckertCBI
Engineering Poplar for Production of Co-Products Muconic Acid and 2-Pyrone-4,6-Dicarboxylic AcidKeaslingJBEIDwivediJBEI
Spatio-Temporal Consumer-Resource and Genome-Scale Metabolic Modeling of the Rhizosphere MicrobiomeNorthenLawrence Berkeley National LaboratoryDukovskim-CAFEs
Tunable Leaky Ribosomal Scanning Governs Translation of Polycistronic Genes in Green AlgaeMerchantUniversity of California–BerkeleyDueñasUniversity
EndoPopulus: Elucidation of the Roles of Diazotrophic Endophyte Communities in Promoting Productivity and Resilience of Populus Through Systems Biology ApproachesDotyUniversity of WashingtonDotyUniversity
High-Throughput Genome Editing and Phenotyping of Plant Cells Using a Scalable and Automated PipelineLeakeyDOE Center for Advanced Bioenergy and Bioproducts InnovationDongCABBI
Deciphering Genetic and Physiological Mechanisms of Nitrogen Use Efficiency in CamelinaLuMontana State University–BozemanDlakicUniversity
Combinatorial Library Design for Improving Isobutanol Production in Saccharomyces cerevisiaeDonohueUniversity of Wisconsin–MadisonDietrichGLBRC
Engineering Novel Microbes for Upcycling Waste PlasticYuanWashington University in St. LouisDiaoUniversity

Videos

m-CAFEs Overview

Dr. Trent Northern discusses an overview of the m-CAFEs SFA at the Lawrence Berkeley National Laboratory.