InCoGenTEC: Intrinsic Control for Genome and Transcriptome Editing in Communities

National Laboratory Project: Sandia National Laboratories

Principal Investigator: Joe Schoeniger¹
Co-Investigators: Kelly William¹, Catharine Mageeney¹, Jesse Cahill¹, Yooli Light¹, Michael Jewett², Farren Isaacs³, Brady Cress^4,Jennifer Doudna⁴
Participating Institutions: ¹Sandia National Laboratories, ²Northwestern University, ³Yale University, ⁴University of California–Berkeley

Summary

Microbial Community Composition. InCoGenTEC researchers are developing technologies to enable the study of changes in microbial community composition and genetics and the engineering of strong, multilayered biocontainment. Led by Sandia National Laboratories (SNL), the project’s technical themes include molecular tools for sensing and regulatory control, flexible genetic cassette design, bacteriophage vectors, and strategies for mapping and characterizing mobile genetic elements and controlling genetic mobility. [Courtesy SNL]

The Intrinsic Control for Genome and Transcriptome Editing in Communities (InCoGenTEC) project focuses on mapping and characterizing mobile genetic elements (MGE) in bacteria and using knowledge of MGE function to develop synthetic genetic elements (SGEs) to selectively and controllably transform bacteria with enhanced biocontainment of heterologous genetic content. Led by Sandia National Laboratories, the InCoGenTEC SFA is generating a database of millions of prokaryotic genomic islands (GIs) and associated DNA integrases with their precise integration sites. This information is used to design digital biology solutions for species-selective chromosome integration and SGE activation, including building SGEs with host-orthogonal transcriptional control coupled to sensors for host gene content. InCoGenTEC is mining its GI databases and analyzing environmental samples to discover bacteriophages capable of transforming diverse, non-model bacterial hosts, and using de novo phage genome synthesis to create transformation vectors capable of efficient selection-free transformation of target bacteria with SGEs. The InCoGenTEC team is engineering new CRISPR-based molecular tools for functional genomics and improved annotation of genomic “dark matter” in phage and other mobile genetic elements discovered through these approaches. The overarching goal of the SFA is to integrate all of these technologies to enable microbiome editing to study and control the composition and function of microbial cultures and communities.

InCoGenTEC also aims to advance safe microbial gene editing by preventing the escape of heterologous/synthetic genetic content in modified microbes. To accomplish this unnecessary heterologous gene content is minimized and site-selective chromosomal integration of SGEs is used to avoid entraining them in natural genetic mobility processes revealed by mobility mapping analysis. Because DNA integrases can enable extremely efficient chromosomal integration, it could be possible to develop selection-free transformation methods that use native integration sites and can be applied in situ without the requirement for troublesome selection markers such as antibiotic resistance genes. In addition, biocontainment of SGEs and modified organisms is enabled by making activation of the SGE dependent on the host cell genetic content, and by implementing SGEs with modular biocontainment features, so that neither escaped genes or organisms can function. The SFA thus combines numerous mechanisms for molecular-context sensing and the regulation of gene expression and DNA recombination to enable stable strain-specific transformation of bacterial cells with enhanced biocontainment. Furthermore, engineered phage vectors that deliver SGEs that sense genetic material may be useful in experiments to detect escaped genes.

The team is designing their approach to enable the combination and modular use of these technologies with multiple layers of biocontainment security in a diverse range of non-model bacterial species found in environmental microbial communities. The SFA outcomes will advance research in understanding and editing microbiomes for biomanufacturing, biomass deconstruction, and soil and water microbiome ecology.

2024 Abstracts

Title	PI	PI Institution	Presenter	Project
Understanding Plant/Environmental Interactions Using Single-Cell Approaches	Cole	DOE Joint Genome Institute	Cole	Early Career
Using Cell-Free Systems to Accelerate Biosystems Design for Carbon-Negative Manufacturing	Jewett	Northwestern University	Choi and Zolkin	University
Converting Methoxy Groups on Lignin-Derived Aromatics from a Toxic Hurdle to a Useful Resource: A Systems-Driven Approach	Marx	University of Idaho	Alleman	University
Mapping Enzymatic Esterification to Natural Expression Levels for a Specialized Clade of HCT Acyltransferases in Poplar	Fox	Great Lakes Bioenergy Research Center	Fox	GLBRC
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in Cyanobacteria	Young	Vanderbilt University	Zuniga	University
Utilizing Cryo-Electron Microscopy to Characterize Proteins Relevant to Biomass Biosynthesis and Bioconversion	Tuskan	CBI	Ziegler	CBI
Investigating Cellular Network and Outer-Membrane Vesicles for the Metabolism of Lignin-Derived Aromatics in Soil Pseudomonas Species	Aristilde	Northwestern University	Zhou	University
Metabolomics Investigates the Impact of Plastic Biodegradation on Mealworm Gut Microbiome	Blenner	University of Delaware	Zhao	University
Transformations of Soil Organic Carbon Influenced by Volatile Organic Compounds	Meredith	University of Arizona	Lunny	University
Using Finlay-Wilkinson Regression to Analyze Genotype–Environment Interaction for Biomass from Switchgrass Field Trials	Juenger	University of Texas–Austin	Zhang	University
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood Decomposer	Zhang	University of Minnesota–Saint Paul	Schilling	University
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion	O’Malley	University of California–Santa Barbara	Zhang	University
Characterizing Bacterial–Fungal Interactions Within Soil Niches and Across Soil Mineralogies	Nguyen	University of Hawai'i–Mānoa	Zeba	University
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene Synthesis	North	The Ohio State University	Young	University
Population Genomic Differentiation of the Ectomycorrhizal Fungus Suillus pungens Along a Climate Gradient	Peay	Stanford University	Yeam	University
Phenotypic and Molecular Characterization of Nitrogen-Responsive Genes in Sorghum	Yang	University of Nebraska–Lincoln	Yang	University
Quantitative Plant Science Initiative: Integrating Functional Genomics with Biomolecular-Level Experimentation to Understand Adaptation to Micronutrient Stress in Poplar and Sorghum	Liu	Brookhaven National Laboratory	Xie	QPSI
Mapping Perturbations in a Naturally Evolved Fungal Garden Microbial Consortium	Burnum-Johnson	Pacific Northwest National Laboratory	Wu	Early Career
Systems-Level Insights into the Physiology of Methane-Fueled Syntrophy Between Anaerobic Methanotrophic Archaea and Sulfate-Reducing Bacteria	Orphan	California Institute of Technology	Mayr	University
Renewed Utility of Tyrosine Integrases	Schoeniger	Sandia National Laboratories	Williams	InCoGenTEC
Optimizing Biological Funneling of Lignin Streams by Comparison in Several Microbial Platforms	Tuskan	CBI	Wilkes	CBI
Plant-Microbe Interfaces: Disentangling Microbial-Mediated Plant Stress Tolerance with Synthetic Communities and Automated Phenotyping	Doktycz	Oak Ridge National Laboratory	Weston	Plant-Microbe Interfaces
Prototyping Carbon-Conserving Networks for Diacid Production	Carothers	University of Washington	Westenberg	University
Molecular and Cellular Responses of Human Endothelial Cells to Low-Dose Radiation	Stevens	Argonne National Laboratory	Weinberg	Low-Dose
Beneficial Plant-Fungal Partnerships in the Resource Economy of Bioenergy Grasses	Stuart	Lawrence Livermore National Laboratory	Nuccio	µBiospheres
Integrated Experimental Approaches to Understand Bioenergy Crop Productivity Through Rhizosphere Processes	Zengler	University of California–San Diego	Northen	University
Amphiphilic Cosolvents Disrupt the Lateral Structure of Model Biomembranes and Reveal an Unrecognized Mode of Cell Stress	Davison	Oak Ridge National Laboratory	Nickels	Biomass Deconstruction
Reactive Transport Modeling for Prediction of Nitrous Oxide Emission from the Subsurface Observatory at a Nitrate-Contaminated Site in Response to Rainfall Events	Adams	Lawrence Berkeley National Laboratory	Newcomer	ENIGMA
Metabolic Remodeling: Stylish Options for Bacterial Interior Design	Neidle	University of Georgia–Athens	Neidle	University
Engineering a Carbon Dioxide Concentrating Mechanism in Cupriavidus necator for Carbon-Negative Biomanufacturing	Jewett	Stanford University–Palo Alto	Nakamura	University
Enabling Synthetic Biology in Setaria and Sorghum Through Targeted Mutagenesis and Programmed Transcriptional Regulation	Baxter	Donald Danforth Plant Science Center	Myers	University
The Enigma of N₂ Fixation in Energy-Limited Anaerobic Methane-Oxidizing Microbial Consortia	Orphan	California Institute of Technology–Pasadena	Murali	University
Engineering Auxenochlorella protothecoides: Artificial Chromosomes, Regulators of Lipid Biosynthesis, and Improving Photosynthesis	Merchant	University of California–Berkeley	Moseley	University
Transgenic Perturbation of Winter-Biased Genes in Populus	Tsai	University of Georgia–Athens	MoradPour	University
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood Traits	Shabek	University of California–Davis	Moe-Lange	University
Understanding the Molecular Rules of Transporter Specificity to Engineer Biofuel-Relevant Efflux Pumps	Donohue	University of Wisconsin–Madison	Miller	GLBRC
Systems Metabolic Engineering of Novosphingobium aromaticivorans for Lignin Valorization	Michener	Oak Ridge National Laboratory	Michener	Early Career
The Plant Synthetic Biology Shared Research Objective: Building a Cross-BRC Repository of Regulatory Elements and Testing Technologies	Donohue	University of Wisconsin–Madison	McKay Whiteman	GLBRC
Model Communities of Soil Microbiomes Reveal Details of Carbon-Use Efficiencies and Interkingdom Interactions Across Scales	Hofmockel	Pacific Northwest National Laboratory	McClure	Phenotypic Response of SOIL Microbes
Mechanisms and Flux Measurements of Microbial Processing of Photosynthetically Fixed Algal Carbon Using Isotope Tracing and Secondary Ion Mass Spectrometry	Stuart	Lawrence Livermore National Laboratory	Mayali	µBiospheres
Flow Sorting and Sequencing Active Environmental Viruses from Methane-Oxidizing Communities with Viral-BONCAT	Orphan	California Institute of Technology–Pasadena	Martinez-Hernandez	University
Evolutionary Flexibility and Rigidity in the Bacterial Methylerythritol Phosphate Pathway	Donohue	University of Wisconsin–Madison	Marshall	GLBRC
Discovery and Functional Characterization of Genomic Islands for Non-model Bacterial Systems	Schoeniger	Sandia National Laboratories	Mageeney	InCoGenTEC
Single-Cell and Spatial Regulatory Map of Poplar	Buell	University of Georgia	Luo	University
The Complex System of Organic Carbon Remineralization in Rapidly Thawing Svalbard Permafrost and Active Layer Soils	Lloyd	University of Tennessee	Lloyd	University
A Prompt Engineering Approach for Root Confocal Image Segmentation Using the Segment Anything Model	Dinneny	Stanford University–Palo Alto	Li	University
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-Fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform Chemicals	Lin	University of Michigan–Ann Arbor	Lin	University
Systems-Level Analysis of Extreme Differences in Fatty Acid Chain-Length Production: Natural Variants and Redesigned Brassicaceae Oilseeds	Cahoon	University of Nebraska–Lincoln	Lingwan	University
Principles Governing Expression of Overlapping Genes	Jiao	Lawrence Livermore National Laboratory	Lim	Microbial Secure Biosystems Design
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome Optimization	Jewett	Northwestern University–Evanston	Liew	University
Massive Protein Redesign to Make Overlapping Genes	Jiao	Lawrence Livermore National Laboratory	Leonard	Microbial Secure Biosystems Design
Advancing Towards Synthetic Biology that Can Detect and Control Plant-Fungal Interactions	Abraham	Oak Ridge National Laboratory	LeBoldus	SEED
Quantitative Trait Locus Mapping of Swarming Motility and Germination Rate in a Bacillus subtilis Library	Tuskan	CBI	Lagergren	CBI
Unraveling Metabolic Interactions Within a Rhizosphere Microbial Community	Zengler	University of California–San Diego	Kumar	University
Influence of Temperature on Arctic Lake Sediment Methane Production and Organic Matter Composition	Varner	University of New Hampshire	Kuhn	University
Natural Diversity Screening, Assay Development, and Characterization of Nylon-6 Enzymatic Depolymerization	Kucharzyk	Battelle Memorial Institute	Beckham	University
Study of the 4-Hydroxybenzoate Catabolic Pathway in White-Rot Fungi via Biochemical and Structural Enzyme Characterization	Salvachúa	National Renewable Energy Laboratory	Kuatsjah	Early Career
Strengthening Educational and Research Capacity for Bioenergy Science at Alabama A & M University through a Combination of Education, Research, and Partnerships	Cebert	Alabama A & M University–Normal	Kuang	RENEW
Harnessing Bacterial-Fungal Interactions to Improve Switchgrass Nitrogen-Use Efficiency	Evans	Michigan State University	Kristy	University
Microbial Networks Demonstrate Extraordinary Metabolic Versatility and the Ability to Obtain Electron Acceptors from Soil Organic Matter in Temperate Peatland Soils	Kostka	Georgia Institute of Technology–Atlanta	Kostka	University
Root Biosynthesis Engineering of the “Plant Diamond” Sporopollenin for Permanent Belowground Carbon Storage	Kirst	University of Florida–Gainesville	Kirst	Energy Earthshots
Charting the Path to Optimize Polysaccharide Accumulation in Bioenergy Sorghum	Donohue	University of Wisconsin–Madison	Kim	GLBRC
Achieving High Productivity of 2-Pyrone-4,6-dicarboxylic acid (PDC) from Aqueous Aromatic Streams with Novosphingobium aromaticivorans	Donohue	University of Wisconsin–Madison	Kim	GLBRC
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic Feedstocks	Soloman	University of Delaware–Newark; Purdue University–West Lafayette	Khim	University
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction, and Function in Knowledgebase	Pett-Ridge	Lawrence Livermore National Laboratory	Marschmann	Microbes Persist SFA
Intraspecific Genetic Variation in Populus trichocarpa Influences Above and Belowground Plant Chemistry and Influences Plant-Soil Interactions	Tuskan	CBI	Kalluri	CBI
Response of Methanotroph Communities to Warming Temperatures in a Recently Thawed Fen	Varner	University of New Hampshire–Durham	Jones	University
Field Observation of Water, Sediment, and Nutrient Distribution Patterns in Alluvial Ridge Basins Between the Abandoned Rio Grande Channels (Resacas)	Dong	University of Texas Rio Grande Valley	Dong	FAIR
Knocking Out a Candidate Gene for Wax Production in Switchgrass Results in an Unexpected Pleiotropic Phenotype	Tuskan	CBI	Devos	CBI
BER-RENEW iSAVe: New Energy Sciences Workforce to Advance Innovations in Sustainable Arid Vegetation	Kalyuzhnaya	San Diego State University	Delherbe	RENEW
Synthetic Biology Tools to Reliably Establish and Monitor Microbial Invasions in the Rhizosphere	Abraham	Oak Ridge National Laboratory	Del Valle Kessra	SEED
ENIGMA Environmental Simulations and Modeling: Predictive Modeling and Mechanistic Understanding of Field Observations	Adams	Lawrence Berkeley National Laboratory	de Raad	ENIGMA
Improving Bioprocess Robustness by Cellular Noise Engineering	Stephanopoulos	Massachusetts Institute of Technology	Daletos	University
Probing the Mechanisms of Microbial Mediated Polymer Deconstruction on the Molecular- and Systems-Level	Rodriguez	UCLA-DOE Institute	Club	University
EndoPopulus: Endophyte Inoculation Alters Whole-Plant Physiology and Growth Dynamics of Populus Under Nitrogen-Deficient Condition	Doty	University of Washington–Seattle	Chung	University
How Soils Work	Pett-Ridge	Lawrence Livermore National Laboratory	Chuckran	Microbes Persist SFA
Developing Reduced Complexity Microbial Communities for Editing Across Scales	Northen	Lawrence Berkeley National Laboratory	Chiniquy	m-CAFEs
Stopping Escape and Malfunction in Genetic Code Engineered Cells	Church	Harvard University	Chiappino-Pepe	University
Connecting Microbial Genotype to Phenotype in Bacterial Strains from a Dynamic Subsurface Ecosystem Using ENIGMA 'Environmental Atlas'	Adams	Lawrence Berkeley National Laboratory	Chakraborty	ENIGMA
Modulating Bioenergy Traits in Field-Grown Sorghum Affects the Rhizosphere Bacterial Communities	Keasling	JBEI	Chai	JBEI
The Fungal Microbiome: Discovering and Investigating Novel Endohyphal Inhabitants	Chain	Los Alamos National Laboratory	Chain	Bacterial-Fungal Interactions
Automation of a CRISPRi Platform for Enhanced Isoprenol Production in Pseudomonas putida	Keasling	JBEI	Carruthers	JBEI
Plant-Microbe Interfaces: Microbially Mediated Host Stress Response—Bridging Field and Laboratory Experiments to Gain Insights into the Populus-Microbiome Symbiosis Under Abiotic Stress	Doktycz	Oak Ridge National Laboratory	Carrell	Plant-Microbe Interfaces
Towards a Mechanistic Understanding of Rhodanobacter Dominance in the Contaminated Subsurface	Adams	Lawrence Berkeley National Laboratory	Carlson	ENIGMA
Knowledge-Guided Interrogation of the Plastid Fatty Acid Biofactory	Cahoon	University of Nebraska–Lincoln	Jorge	University
Development of High-Throughput Methods to Assist Measure of Biological Nitrification Inhibition in Populus Soils	Cahill	Oak Ridge National Laboratory	Cahill	Early Career
Metabolic Engineering of Issatchenkia orientalis for Cost-Effective Production of Citramalate	Leakey	CABBI	Bun	CABBI
BioPoplar: A Tunable Chassis for Diversified Bioproduct Production	Robin Buell	University of Georgia–Athens	Robin Buell	University
Lipid Membrane Biology of Microbial Cell Factories During Microaerobic Fermentation	Budin	University of California–San Diego	Budin	Early Career
Engineering Continuous Trait Variation in Bioenergy Feedstocks to Optimize Growth on Marginal Lands	Brophy	Stanford University	Brophy	Early Career
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve Productivity	Leonelli	University of Illinois Urbana-Champaign	Brooks	University
Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon Cycling	Nuccio	Lawrence Livermore National Laboratory	Brisson	Early Career
Assessing the Effect of Nitrogen and Phosphorus Fertilization on Root-Microbial Communities and Yield Response in Sorghum bicolor	Bennetzen	University of Georgia–Athens	Brailey-Jones	University
A Systems Approach for Predicting Metabolic Fluxes in Auxenochlorella protothecoides	Merchant	University of California–Berkeley	Boyle	University
Rendering the Metabolic Wiring Powering Wetland Soil Methane Production	Wrighton	Colorado State University–Fort Collins	Borton	University
Unraveling Microbial and Viral Responses to Wetting Using Multiomics	Pett-Ridge	Lawrence Livermore National Laboratory	Blazewicz	Microbes Persist SFA
Climate vs. Energy Security: Quantifying the Trade-Offs of BECCS Deployment and Overcoming Opportunity Costs on Set-Aside Land	Leakey	CABBI	Blanc-Betes	CABBI
Beyond Boundaries: Foxtail Mosaic Virus Drives Heterologous Protein Expression and Precision Gene Editing in Sorghum	Leakey	CABBI	Baysal	CABBI
Characterizing Mechanistic Roles of Viruses in Driving Biogeochemical Cycles in the Rhizosphere	Mouncey	Lawrence Berkeley National Laboratory	Basson	JGI
Performance Thresholds for Co-Utilization of Lignin-Derived Aromatics and Sugars	Keasling	JBEI	Baral	JBEI
Response of Soil Microbial Communities to Nitrogen and Phosphorus Input in Sorghum Field	Bennetzen	University of Georgia–Athens	Babalola	University
The Lawrence Livermore National Laboratory Cryo-NanoSIMS: The Next Generation for High Spatial Resolution Functional Analysis	Stuart	Lawrence Livermore National Laboratory	Weber	µBiospheres
Applying Metabolic Models to Mechanistically Understand and Predict Interactions Between Anaerobic Methanotrophic Archaea and Sulfate-Reducing Bacteria Strains in Geochemical Cycling Processes	Henry	Argonne National Laboratory	Liu	University
Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems	Guarnieri	National Renewable Energy Laboratory	Arnolds	IMAGINE BioSecurity
Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis Applications	Yung	Lawrence Livermore National Laboratory	Wackelin	Early Career
Identification of the Genetic Factors that Contribute to Biological Nitrogen Fixation in Sorghum (Sorghum bicolor)	Ane	University of Wisconsin–Madison	Venado	University
Drought-Induced Plant Physiology Drives Altered Microbe-Metabolite Interactions Along the Plant Rhizosphere Column	Egbert	Pacific Northwest National Laboratory	Anthony	Persistence Control of Soil Microbiomes
Enhancing Biological Nitrogen Fixation in Sorghum (Sorghum bicolor) Aerial Roots Through Engineering Diazotrophic Communities	Ane	University of Wisconsin–Madison	Venado	University
Vision-Driven RhizoNet: Foundations for Systematic Measurement of Plant Root Biomass	Tringe	Lawrence Berkeley National Laboratory	Ushizima	EERC
How Microbes and Minerals Make Necromass that Persists	DeAngelis	University of Massachusetts–Amherst	Anderson	University
Functional Characterization of GT47 Glycosyltransferases in Duckweed to Facilitate Predictive Biology	Urbanowicz	University of Georgia	Urbanowicz	University
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic Rubber	Tullman-Ercek	Northwester University	Tullman-Ercek	University
Exploring the Metabolic Capability of Undomesticated Thermophilic Bacillus coagulans for Biosynthesis of Designer Esters at Elevated Temperatures	Trinh	University of Tennessee–Knoxville	Trinh	University
Multiscale Computational Digital Twins for Whole-Body to Subcellular Radiation Effects	Stevens	Argonne National Laboratory	Agasthya	Low-Dose
RESTOR-C: Center for Restoration of Soil Carbon by Precision Biological Strategies	Tringe	Lawrence Berkeley National Laboratory	Tringe	EERC
High (School) Throughput Screening of BAHD Transferases	Acheson	University of Wisconsin–Madison	Acheson	GLBRC
Understanding the Role of Permafrost-Affected Microbes in Thawing Arctic	Lloyd	University of Tennessee–Knoxville	Abuah	University
Understanding Microbial Invasion Biology from Laboratory-to-Field for Secure Ecosystem Engineering and Design	Abraham	Oak Ridge National Laboratory	Abraham	SEED
Progress Towards the Generation of Oily Miscanthus	Leakey	University of Illinois Urbana–Champaign	Trieu	CABBI
Developing Temperature-Jump X-Ray Crystallography to Study Dynamic Biosynthetic Enzymes at Synchrotrons and X-Ray Free-Electron Lasers	Thompson	University of California–Merced	Thompson	FAIR
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel Production	Zengler	University of California–San Diego	Thiruppathy	University
CRISPR Activation of Poplar Target of Rapamycin Genes Improves Nitrogen Use Efficiency and Indicates Possible Functional Divergence	Coleman	University of Maryland	Tayengwa	University
From Viromes to Virocells: Dissecting Viral Roles in Terrestrial Microbiomes and Nutrient Cycling	Sullivan	The Ohio State University	Sullivan	University
Iron-Mediated Microbial Interactions with Primary Producers in Terrestrial and Aquatic Systems	Stuart	Lawrence Livermore National Laboratory	Stuart	µBiospheres
AI Foundation Models for Understanding Cellular Responses to Radiation Exposure	Stevens	Argonne National Laboratory	Stroka	Low-Dose
Cryosectioning-Enabled Super-Resolution Microscopy for Studying Nuclear Architecture at the Single Protein Level	Church	Harvard Medical School	Stein	University
Understanding the Role of Tolerance on Microbial Production of Isoprenol	Keasling	JBEI	Srinivasan	JBEI
Leveraging Type I-F CRISPR-Associated Transposase Regulators to Improve Editing Efficiency	Northen	Lawrence Berkeley National Laboratory	Song	m-CAFEs
Interactions Between Enhanced Rock Weathering and Soil Organic Carbon Cycling in Coordinated, National-Scale Field Trials	Pett-Ridge	Lawrence Livermore National Laboratory	Sokol	EERC
Synthetic Biology Tool Development for Precision Engineering of Oilseed Crops	Cahoon	University of Nebraska–Lincoln	Smanski	University
Multiomics-Driven Microbial Model Optimization	Carothers	University of Washington–Seattle	Shin	University
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil Carbon	Meredith	Lawrence Berkeley National Laboratory	Shen	University
Microbial Treatments to Increase Carbon Sequestration in Biofuel Crop Systems	Tringe	Lawrence Berkeley National Laboratory	Sevanto
Global Proteomics and Resource Allocation Modeling Reveals Thermodynamic Bottleneck and Highlights Effective Genetic and Metabolic Interventions for C. thermocellum	Tuskan	CBI	Schroeder	CBI
Leveraging Leaf Structure and Biochemistry to Enhance Water Use Efficiency in Sorghum	Baxter	Donald Danforth Plant Science Center	Schrader	University
Computational Modeling to Enable Predictive Secure Biosystems Designs	Guarnieri	National Renewable Energy Laboratory	Santibanez Palominos	IMAGINE BioSecurity
Understanding the Role of Duckweed Transcription Factor in Triacylglycerol Metabolism and Abiotic Stress Tolerance in Plants	Muthan	West Virginia State University	Sanjaya	FAIR
Designing Novel Enzymes for Complete Degradation of Recalcitrant Polyamides	Zanghellini	Arzeda Corporation	Sangha
Real-Time Sensing and Adaptive Computing to Elucidate Microenvironment-Induced Cell Heterogeneities and Accelerate Scalable Bioprocesses	Salvachúa	National Renewable Energy Laboratory	Salvachúa	Accelerate
Extracting Switchgrass Features Through Minirhizotron and Hyperspectral Image Processing	Juenger	University of Texas–Austin	Saldanha	University
Plant-Microbe Interfaces: Specialized Fungal Metabolites Regulate Synthetic Fungal Communities and Their Interactions with Populus	Doktycz	Oak Ridge National Laboratory	Rush	Plant-Microbe Interfaces
Multiomics Pipelines and Approaches to Characterize Viral Impacts on Environmental Microbiomes	Roux	DOE Joint Genome Institute	Roux	Early Career
Mapping Toxin-Antitoxin Systems for Microbial Community Biocontainment	Jiao	Lawrence Livermore National Laboratory	Ricci	Microbial Secure Biosystems Design
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping Datasets	Rellán-Álvarez	North Carolina State University	Rellán-Álvarez	University
Microbial Responses to Scaling Complexity in Chitin Decomposition with Changing Moisture and Structure Levels	Hofmockel	Pacific Northwest National Laboratory	Reichart	Phenotypic Response of SOIL Microbes
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic Stress	Cregger	Oak Ridge National Laboratory	Ramírez-Flores	Early Career
Using Biodiversity to Explore the Diversification of Environment-Regulated Growth	Dinneny	Stanford University	Ramachandran	University
Structural Characterization of GT47 Glycosyltransferases in Duckweed to Facilitate Predictive Biology	Urbanowicz	National Renewable Energy Laboratory	Prabhakar	University
Transcriptional Profiling of Winter-Regulated Genes in Populus trichocarpa	Tsai	University of Georgia	Ployet	University
Characterization, Neutron Scattering, and Molecular Dynamic Simulation of the Lignin Carbohydrate Complex Structure and its Disruption	Davison	University of Tennessee–Knoxville	Venkatesh Pingali	Biomass Deconstruction
Terraforming Soil Energy Earthshot Research Center: Accelerating Soil-Based Carbon Drawdown Through Advanced Genomics and Geochemistry	Pett-Ridge	Lawrence Livermore National Laboratory	Pett-Ridge	EERC
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production	Peter	University of Florida	Peter	University
Plant-Microbe Interfaces: Defining Quorum Sensing Signal Potential in the Populus Microbiome and Examining its Role in Community Selection and Structure	Doktycz	Oak Ridge National Laboratory	Pelletier	Plant-Microbe Interfaces
The Root Microbiome of Camelina: From Structure to Function	Lu	Montana State University	Paulitz	University
Friends and Foes: How Microbial Predators Influence Nutrient Cycling in Soil	Hungate	Northern Arizona University	Patel	University
Deciphering Stress-Resilient Growth in Brassicaceae Models: A Comparative Genomics Analysis of Adaptative on to Extreme Environments	Dinneny	Stanford University	Pantha	University
Unleashing Photosynthesis and Nitrogen Fixation for Carbon Neutral Production of Nitrogen-Rich Compounds	Pakrasi	Washington University in St. Louis	Pakrasi	Energy Earthshots
Conversion of Lignocellulosic Plant Biomass into Industrial Chemicals via Metabolic Engineering of Two Extreme Thermophiles, Caldicellulosiruptor bescii and Pyrococcus furiosus	Adams	University of Georgia	O'Quinn	University
Developing Chassis for Low Density Polyethylene Upcycling from Microbes Native to the Gut Microbiome of Yellow Mealworms	Blenner	University of Delaware	Ott	University
Cell-Free Systems Biology: Characterizing Pyruvate Metabolism of Clostridium thermocellum with a Three-Enzyme Cascade Reaction	Olson	Dartmouth College	Olson	University
Bacterial Degradation of Sorgoleone, a Step Towards Enforcing Rhizobacteria Containment	Egbert	Pacific Northwest National Laboratory	Oda	Persistence 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 Biocontainment	Church	Harvard Medical School	Nyerges	University
Assessing Bacterial-Fungal Interactions Across Experimental Scales	Chain	Los Alamos National Laboratory	Johnson	Bacterial-Fungal Interactions
Sequencing Driven Accelerated Discovery of Genes Regulating Water Use Efficiency and Stomatal Patterning and in C₄ Crops with High-Throughput Phenotyping	Baxter	Donald Danforth Plant Science Center	Jiang	University
Reduced Environmental Plasticity in Pennycress Improves Responses to Competition and Climate Change	Sedbrook	Illinois State University	Jawahir	University
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic Pathways	Jarboe	Iowa State University	Jarboe	University
Multichromatic Optogenetic Control of Microbial Co-Culture Populations for Chemical Production	Avalos	Princeton University	Jang	University
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum Biomass	Kirst	University of Florida	Pereira	University
Conversion of Natural and Transgenic Sugarcane and Poplar Variants with an Ionic-Liquid-Based Feedstocks-To-Fuels Pipeline	Keasling	JBEI	Islam	JBEI
Engineering Inducible Biological Nitrogen Fixation for Bioenergy Crops	Donohue	DOE Great Lakes Bioenergy Research Center	Infante	GLBRC
Role of Nitrogen Oxides in a High Nitrate and Heavy Metal Contaminated Field Site: What Has Been Observed and What Researchers Aim to Understand	Adams	Lawrence Berkeley National Laboratory	Hunt	ENIGMA
Machine Learning-Assisted Genome-Wide Association Study Uncovers Copy-Number Variations of Tandem Paralogs Driving Stress Tolerance Evolution in Issatchenckia orientalis	Leakey	DOE Center for Bioenergy and Bioproducts Innovation	Hsieh	CABBI
Comparison of Soil Responses to Long-Term Fertilization and Short-Term Nitrogen and Carbon Amendments in Miscanthus and Corn	Leakey	DOE Center for Advanced Bioenergy and Bioproducts Innovation	Howe	CABBI
Drought Influences Microbial Activity and the Accrual and Composition of Soil Organic Carbon	Pett-Ridge	Lawrence Livermore National Laboratory	Honecker	Microbes Persist SFA
Profiling Temporal and Spatial Activities of Rhizobacteria	Adams	DOE Joint Genome Institute	Honda	JGI
Metabo-Lipidomics Unveil Root Exudate Molecular Diversity and Functional Impacts on Soil Microbial Communities	Hofmockel	Pacific Northwest National Laboratory	Hofmockel	Phenotypic Response of SOIL Microbes
Legacy Effects of Warming Alter Simple and Complex Soil Organic Matter Decomposition	Hungate	Northern Arizona University	Hoffman	University
Plant-Microbe Interfaces: Unraveling How Microbial Adaptation Strategies Are Shaped by the Chemical Environment of the Populus Rhizosphere	Doktycz	Oak Ridge National Laboratory	Hettich	Plant-Microbe Interfaces
Dissecting Bacterial-Fungal Interactions in the Bouteloua gracilis Rhizosphere Microbiome Using Metabolic Phenotyping	Chain	Los Alamos National Laboratory	Hanson	Bacterial-Fungal Interactions
Plastic Degradation and Upcycling by the Gut Microbiome of Yellow Mealworms	Solomon	University of Delaware	Hansen	University
CRISPR/Cas Tool Development and Genome Engineering in Nonmodel Bacteria	Carothers	University of Washington	Guzman	University
EcoFAB 3.0: A Controlled Ecosystem for Bioenergy Crops	Keasling	JBEI	Gupta	JBEI
IMAGINE BioSecurity: Genome-Scale Engineering and High-Throughput Screening to Establish Secure Biosystems Design	Guarnieri	National Renewable Energy Laboratory	Guarnieri	IMAGINE BioSecurity
Physical and Molecular Responses of Pennycress (Thlaspi arvense L.) to Waterlogging	Sedbrook	Illinois State University	Gschwend	University
Analyzing Biotic and Abiotic Stress Responses in Sorghum Using Comprehensive Field Phenomics Data	Eveland	Donald Danforth Plant Science Center	Gonzalez	University
Pyrocosms to Measure Influence of Fire Intensity, Time, and Soil Depth on Microbial Succession, Cross-Kingdom Interactions, and Greenhouse Gas Emissions	Glassman	University of California–Riverside	Glassman	University
Optimizing Enzymes for Plastic Upcycling Using Machine Learning Design and High Throughput Experiments	Gauthier	Harvard Medical School	Gauthier	University
Engineering Cupriavidus necator for Efficient Aerobic Conversion of Carbon Dioxide (CO₂) to Fuels and Chemicals	Jewett	Stanford University	Fulk	University
Engineering C₄ Feedstock Crops for Improved Water Use Efficiency and Drought Avoidance	Baxter	Donald Danforth Plant Science Center	Fischer	University
Integrating Molecular Genetics and Precision Phenotyping to Elucidate the Genetic Basis for Drought Resilience in Sorghum	Eveland	Donald Danforth Plant Science Center	Eveland	University
Dead or (Still Not) Alive: Patterns and Drivers of Soil Viral Activity, Turnover, and Decay	Emerson	University of California–Davis	Emerson	University
Reinforced CRISPR Interference (CRISPRi) Enables Reliable Multiplex Gene Repression In Phylogenetically Distant Bacteria	Egbert	Pacific Northwest National Laboratory	Elmore	Persistence Control of Soil Microbiomes
Surveying, Culturing, and Sequencing Root Microbiomes Associated with Switchgrass, a Native North American Biofuel Feedstock	Juenger	University of Texas–Austin	Edwards	University
Unveiling Molecular Interactions and Metabolic Contributions in Sorghum Anthracnose Defense: Towards the Integration of Fungal Pathogen and Host Sorghum Models	Liu	Brookhaven National Laboratory	Edirisinghe	BRaVE
Systems Framework to Enhance the Potential of Camelina as Oilseed Crop	Grotewold	Michigan State University	Edger	University
Thermophilic Genetic Tool Development for Engineering and Functional Genomics in Clostridium thermocellum	Tuskan	CBI	Eckert	CBI
Engineering Poplar for Production of Co-Products Muconic Acid and 2-Pyrone-4,6-Dicarboxylic Acid	Keasling	JBEI	Dwivedi	JBEI
Spatio-Temporal Consumer-Resource and Genome-Scale Metabolic Modeling of the Rhizosphere Microbiome	Northen	Lawrence Berkeley National Laboratory	Dukovski	m-CAFEs
Tunable Leaky Ribosomal Scanning Governs Translation of Polycistronic Genes in Green Algae	Merchant	University of California–Berkeley	Dueñas	University
EndoPopulus: Elucidation of the Roles of Diazotrophic Endophyte Communities in Promoting Productivity and Resilience of Populus Through Systems Biology Approaches	Doty	University of Washington	Doty	University
High-Throughput Genome Editing and Phenotyping of Plant Cells Using a Scalable and Automated Pipeline	Leakey	DOE Center for Advanced Bioenergy and Bioproducts Innovation	Dong	CABBI
Deciphering Genetic and Physiological Mechanisms of Nitrogen Use Efficiency in Camelina	Lu	Montana State University–Bozeman	Dlakic	University
Combinatorial Library Design for Improving Isobutanol Production in Saccharomyces cerevisiae	Donohue	University of Wisconsin–Madison	Dietrich	GLBRC
Engineering Novel Microbes for Upcycling Waste Plastic	Yuan	Washington University in St. Louis	Diao	University