Microbiome Research For Carbon Cycling And Sustainable Bioenergy .

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Microbiome Research for Carbon Cycling and Sustainable Bioenergy Feedstocksin BER's Genomic Science ProgramBoris WawrikU.S. Department of Energy (DOE), Office of Science (SC)Biological and Environmental Research (BER)Biological Systems Science Division (BSSD)

Integrate observations and experimental capabilitiesfor predictive systems-level understanding, frommicrobes and plants to ecosystems and the earth systemBiological Systems Science DivisionDivision Director: Todd Anderson Bioenergy Research Centers Genomic Science Program Biomolecular CharacterizationImaging Science Structural Biology Joint Genome InstituteEarth and Environmental System ScienceDivision Director: Gary Geernaert Atmospheric System ResearchEnvironmental System ScienceClimate & Earth System ModelingFacilities & InfrastructureEnvironmental Molec. Sciences LabARM Climate Research Facility

Biological Systems Science Division (BSSD)MISSION: to provide the necessary fundamental science to understand, predict, manipulate, and design biologicalprocesses that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural,environmental processes relevant to DOE. Bioenergy Research Centers Sustainable Bioenergy Feedstock Development Plant Genomics Deconstruction Microbial Conversion Synthetic Biology Innovative ways forbioproduction of fuels,chemicals, and biomaterials Modeling and HTP DBTL Secure Biodesign Microbial Systems Biology Natural and SyntheticMicrobial Consortia Techniques and TechnologyBioenergy ResearchBiosystems DesignMicrobiome Science Computational Biology Biomolecular Characterization and Imaging Science DOE User Facilities (JGI, EMSL, Light & Neutron Sources)Enabling Capabilities

The Genomic Science Program (GSP) What information is encoded in a genome sequence, andhow can genomes be interpreted to explain the functionalcharacteristics of cells, organisms, and whole biologicalsystems? How do interactions among cells regulate the functionalbehavior of living systems, and how can these interactionsbe understood dynamically and predictively? How do plants, microbiomes, and communities of organismsadapt and respond to environmental conditions (e.g.,temperature, water, nutrient availability, and ecologicalinteractions), and how can their behavior be manipulatedtoward desired outcomes? What organizing principles need to be understood tofacilitate the design and engineering of new biologicalsystems for beneficial purposes?

Sustainable Biomass Production - Research to Advance Bioenergy AgricultureIntegrated lab and field experiments (field work required)Enhance biomass productivityThe impacts of bioenergy cropping systems on the local ecosystemImpact of changing environmental conditionsMolecular and physiological mechanisms that control bioenergy crop vigor resource use efficiency resilience/adaptability to abiotic stress Role of microbial communities in plant-soil environment Microbiome role in plant performance What role does the microbiome play in plant performance ? What are the mechanisms of plant-microbe interactions ? How can microbial traits be leveraged to enhance sustainability?

Example - Technology Integration to Standardize Microbiome ExperimentsEcoFABs Controlled model ecosystems in which microbesand host responses can be monitored High replicability Allows automation Can integrate imaging systems approachesAn EcoFab device containing artificial soil and a plant seedling. HTPsampling and detection can be achieved with the EcoBOT.https://eco-fab.org/Rhizosphere-on-a-chip Tractable approach for studying carbon hotspotformation and plant-microbe interactions in soils. Create a synthetic soil habitat that enables dynamicimaging and spatial chemical sampling of plant roots.A Brachypodium seedling growth in the rhizosphereon-a-chip. Hotspots of exuded amino acids aredetected within the rhizosphere.

Biosystems Design – Systems Biology and Genome Engineering Basic Research Design and engineer new biological systemsInnovative bioproduction of fuels, chemicals, and biomaterialsEngineer microbes, plants, and microbial consortiaGenome-scale engineeringDevelop novel in vivo and cell-free engineering toolsCreate new biological functionsDevelopment of new platform organisms for genome engineeringHigh-throughput approaches for screening and testingUpcycling of synthetic polymersSecure bio-design

Examples - Secure Biosystems Design ProjectsSecure and Robust Biosystems Design forEnvironmental Microorganisms (LLNL) reduce the risk of unintended ecological consequencesfrom environmentally deployed genetically engineeredmicroorganisms (GEMs)design multilayered containment strategies for GEMs inthe rhizosphereadvance synthetic gene entanglement strategy forcontainmentPersistence Control of Engineered Functions inComplex Soil Microbiomes (PNNL) design the environmental niche of bacteria throughgenome reductiondetermine the genetic, metabolic, and spatial factorsthat control microbial persistence in the rhizospheredevelop genetic tools for phylogenetically diverserhizosphere bacteriaDesign metabolic addiction strategies for GEMsBiological and Environmental Research

Environmental Microbiome ResearchMicrobial activity relevant to biogeochemical processesSystems-level research on nutrient and carbon cyclingMechanistic underpinnings of microbial activitiesInteractions of viruses, bacteria, archaea, plant, fungi, andprotists ‘omics-based high-resolution, high-throughput techniquesand technologies Integrate microbial processes across scale via computationaland modeling approaches Develop a predictive understanding of microbial systemsbehavior in terrestrial soil ecosystems -- including thecycling, release, and storage of C in soils

Soil C-cycling Projects in the Environmental Microbiome PortfolioMicrobial degradationof pyrogenic organicmatterImpact of elementalcycles e.g. P or Cu onC and N cyclesInterkingdominteractions in soilC cyclingThe role of protists inorganic matter turnoverThe role of virusesin soil C cyclingMicrobial traits andmodels of behavior atthe macro scaleTools to studyanaerobic methanemetabolismMicrobial adaptionand evolution todrought in soilsMicrobial C cycling inthawing permafrostMetabolic exchangein soils, wetlands, andartificial ecosystems

The Joint Genome Institute (JGI) DNA sequencing of fungal, algal, bacterial, archaeal, viral and plant genomes;community shotgun DNA/RNA; 16S; Whole genome DNA methylation analysis Transcriptomics; non-coding RNA (both small and long ncRNA)characterization; Fluorescence activated cell sorting; single-cell genomics DNA/gene synthesis; assembly of biosynthetic pathways in heterologous hosts CRISPR-based gRNA library construction and QC. Mass spectrometry-based metabolomics Analysis pipelines for the datasets above Technology DevelopmentRoot associatedmicrobeEucalyptus grandisSetaria viridisA. muscariaSupport projects through Community Sequencing Program (CSP) Call.Collaborative funding with EMSL via the JGI-EMSL FICUS (Facilities IntegratingCollaborations for User Science) program.Updated: Tree of LifeEpigenomics

Bioimaging and CharacterizationVisualization across scales of observation to biomolecules Develop in situ, dynamic, and nondestructive multifunctional imaging Create enabling visualization and characterization capabilities Combine biomolecular structural characterization with genomics information and bioinformaticsto infer function and improve genome annotation or design new functions. Visualize expressed biomolecules within living plant or microbial cells or within microbialcommunities. Quantum imaging

Computational BiologyGoal is to support the development of computational and instrumental platforms to enablebroader integration and analysis of large-scale complex data within BER’s multidisciplinaryresearch efforts. Assemble capabilities for the processing of large, complex, andheterogeneous systems biology data.Create the next generation data systems and algorithms that connectobservations across scales of molecular, structural, genomic, and other omicsdata with cellular and multicellular processes.Develop explainable artificial intelligence (XAI) algorithms to identifyrelationships among different parts of genomesCreate techniques to process and integrate imaging and structural biologydata with simulation and other biological measurements.Advanced simulation capabilities to model key processes occurring within oramong cells building towards whole-cell simulation.Assemble an integrated systems biology virtual laboratory to accelerate insilico ideation and collaboration within the research community.


Microbiome Research for Carbon Cycling and Sustainable Bioenergy Feedstocks in Biological and Environmental Research's Genomic Science Program presentation by Boris Wawrik, DOE, Office of Science, Biological and Environmental Research, at the Bioenergy's \ Role in Soil Carbon Storage Workshop held March 28th 29th, 2022. Created Date

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