Q&A with Carrie Eckert: Designing microbes for biomanufacturing success

Carrie Eckert is working toward a future in which engineered microbes and plants are the workhorses of ultra-efficient biofactories, turning biomass into high-value products. As co-chief science officer for the Department of Energy's Center for Bioenergy Innovation (CBI) at Oak Ridge National Laboratory, she is stewarding a team of scientists across the country who are making that vision a reality.

Eckert brings her expertise as head of the Synthetic Biology section at ORNL to direct a growing lexicon of new approaches and tools to the task of engineering microbes for industrial-scale bioprocessing. She is working with colleagues at ORNL as well as with CBI researchers at academic, national lab, and industrial partners across the nation to fine-tune these microorganisms for the breakdown and conversion of plant biomass into reliable, domestic sources of new fuels, chemicals and materials.

Eckert shared achievements so far and what she's looking forward to as scientists increase the pace of their research, harnessing artificial intelligence, machine learning and automation to deliver fundamental science that can scale from discovery to deployment for tomorrow's factories.

Q: What is CBI's mission and approach in support of a stronger bioeconomy?

A: CBI has a core vision of a thriving bioeconomy based on U.S. resources and biotechnological prowess, providing a secure, domestic supply of valuable products at prices that make sense.

CBI is developing science-based solutions for low-cost, high-yield manufacturing of biofuels and bioproducts. We're tackling this on two key fronts: developing better dedicated biomass crops like perennial poplar trees and switchgrass and building better microbes to break down and process plant biomass. We then use catalytic approaches to turn the resulting chemical compounds into desired products.

We have developed biotechnologies that make the overall manufacturing process cheaper, such as feedstock crops that need less water and nutrients to grow larger, and processing methods that reduce or negate the need for costly solvents.

Our structure, bringing together scientists and engineers from multiple disciplines across the country, reflects the big-team-science approach that time and again has resolved some of the toughest scientific challenges for the nation's economic success.

Q: What are some of CBI's recent discoveries for the bioeconomy?

A: Most recently, we demonstrated a proof of concept utilizing all the parts of plant biomass and our engineered microbes to produce ethanol and other intermediates that were catalytically upgraded into components for sustainable aviation fuel. That accomplishment was a direct result of our integrating expertise across plant biology and genomics, synthetic biology, chemistry and catalysis expertise, just to name a few of the disciplines we bring together under the CBI umbrella. We also put candidate fuels through their paces by submitting them for Tier 1 evaluation - ensuring their basic chemistry and physical properties are compatible as drop-in fuels for jet aircraft.

On the feedstocks side, our plant scientists recently discovered a gene in poplar called Booster that enhances photosynthesis. When we created hybrid trees with Booster, they grew 200 percent taller in the greenhouse and up to 37 percent taller in the field, with as much as 88 percent more stem volume, significantly increasing biomass per tree. We've also made genetic discoveries for feedstocks that are tolerant of drought and scarce nutrients - important for dedicated crops that can be grown on what we call marginal lands, not used for growing food.

Q: What sets CBI apart in the synthetic biology space?

A: What sets us apart in synthetic biology is the breadth of organisms we work with. There's already a wide body of knowledge out there about model microbial strains like E. coli and model plants like Arabidopsis. But we're focused on harder, non-model targets - organisms that have natural traits amenable to the bioprocesses we are engineering. CBI has, for instance, focused on wild-type microbes that are naturally good at digesting and converting components of plant biomass such as cellulose and lignin polymers. These microbes are robust and typically have some resistance to stressors present in industrial processes. As those traits are difficult to engineer into model systems, we have focused on developing the enabling genetic tools to directly engineer these non-model organisms. In CBI and at ORNL, we've utilized these tools to build sturdier, more effective microbial engines as well as more resilient plant feedstocks.

We recently published a perspective of our achievements in this space, as well as future research opportunities to support biomanufacturing, in Biotechnology Advances. The paper ["Building an expanded bio-based economy through synthetic biology"] provides a comprehensive roadmap for an expanded bioeconomy by integrating advances in synbio across both microbes and plants. It describes the ways that we're rapidly accelerating the design-build-test-learn cycle by developing genetic tools and employing enabling technologies like automation and AI/ML for faster discoveries.

Q. What are some of the tools we've developed to customize target microbes?

A. We've developed high-throughput tools for customizing Pseudomonas putida, a stress-resistant microbe that's good at converting plant biomass components into biofuels and bioproducts. We've developed high-throughput CRISPR interference (CRISPRi) libraries that can help us pinpoint which of P. putida's genes control desirable traits. CRISPRi lets us turn genes down or temporarily switch them off, without cutting DNA. That allows us to systematically test what thousands of genes do and fine-tune the microbe's cells for specific tasks, and provides rich datasets for AI/ML discovery and prediction.

We've also advanced the ability to engineer a difficult but very valuable organism, Clostridium thermocellum. C. therm thrives at high temperatures and doesn't need oxygen to grow, lowering contamination risk and needing less energy for cooling in biorefineries. It natively breaks down cellulose - the tough structural materials in plant cell walls - while reducing reliance on added enzyme cocktails, avoiding extra cost and pretreatment. These characteristics make the microbe ideal for industrial-scale biomanufacturing using CBI's low-cost consolidated bioprocessing approach that combines biomass deconstruction and fermentation in a single step.

We've made great strides in optimizing C. therm. This is where our development of SAGE tools come in, specifically the Thermostable Serine Recombinase-Assisted Genome Engineering platform (tSAGE), that we built at ORNL. It's a method that lets us rapidly insert DNA into the microbe's chromosome in days instead of the weeks required with traditional methods, allowing us to evaluate libraries of promoters that act like genetic on/off switches to more effectively control gene expression. We've also optimized CRISPR-Cas genome editing for C. therm and can suppress targeted gene expression with the CRISPRi method to mirror library efforts developed in P. putida. Our tools have enabled faster and more high-throughput strain design and testing and more comprehensive genetic control, providing genetic parts for pathway engineering, as well as data required for AI/ML methods.

Q: What's ahead for CBI in the synthetic biology space?

A: We are increasingly looking to AI and automation to accelerate our discoveries in alignment with the DOE Genesis Mission. We're deploying synthetic biology and phenotyping capabilities to increase automation and throughput, and then leveraging machine learning and AI to rapidly assess the resulting data and provide further targets for validation using automated, high-throughput phenotypic pipelines towards engineering efforts.

Our synbio tools, high-throughput microbial transformation facility, and advanced proteomics and other characterization systems available at ORNL and within the larger national lab system assist us as we transform and assess microbial strains in parallel, analyze growth rates, substrate utilization, product formation and stress tolerance, comparing variants under tightly controlled conditions.

We've set up a system to create and evaluate 96 targeted mutant transformations at a time to figure out the best pathways and growth/production tradeoffs. The more data we have in hand the better, so that our machine learning and AI modeling strategies can help us understand and predict new targets.

On the plant transformation side, we've got a fantastic capability in the automated APPL facility [Advanced Plant Phenotyping Laboratory] here at ORNL that's giving us a wealth of knowledge on plant genetics and performance to speed our crop engineering research. APPL is also part of a multi-lab Genesis project called OPAL [Orchestrated Platform for Autonomous Laboratories] that has already demonstrated an early agentic AI milestone.

We're working closely with computational scientists to bring together the experimentalists who are generating data with the AI modelers who are optimizing that data for faster insights.

Q: What are you excited about as you take on the role of CBI co-chief science officer?

A: I've always enjoyed being part of the science team at CBI. But as chief science officer for deconstruction and conversion, I get to focus on the breadth of our research - to see the whole rather than just my own science domain. Being engaged in all the processes at CBI lets me see how all the parts fit together, and that's very exciting. My goals are to keep that wide view, to listen to all of our scientists and stakeholders, make sure we're staying on top in our science, and to help drive where we're going and how we get there.

Learn more about the Center for Bioenergy Innovation.

The Genesis Mission is DOE's national initiative to build the world's most powerful scientific platform to accelerate discovery science, strengthen national security, and drive energy innovation. It does so by enabling AI-driven, exascale-powered advances that enhance America's energy innovation, global competitiveness and security.

UT-Battelle manages ORNL for DOE's Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The Office of Science is working to address some of the most pressing challenges of our time. For more information, visit energy.gov/science. - Stephanie Seay