CABBI: Center for Advanced Bioenergy and Bioproducts Innovation

The Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), led by the University of Illinois Urbana-Champaign, has substantially developed scientific understanding and technological innovations required to produce economically and ecologically sustainable liquid biofuels and platform chemicals. Production system sustainability is guided and evaluated by models that integrate technoeconomic assessment (TEA) and life-cycle assessment (LCA), which are tools informed by cutting-edge measurements of agroecosystem function and industrially relevant process data. Researchers pursue a vision of “plants as factories,” in which biofuels, bioproducts, and foundation molecules are directly synthesized by highly productive, resilient, and sustainable grass feedstocks carrying out efficient C4 photosynthesis. Plant-derived oils and sugars are further upgraded to high-value platform compounds by highly engineered nonmodel yeasts. CABBI’s research approach maximizes team expertise in ecosystem ecology, agricultural economics, agronomy, plant and microbial engineering, bioprocessing, genomics, and computational biology.

Over the last 5 years, CABBI has advanced transformative technologies for the economic and sustainable production of biofuels and bioproducts from plants by pursuing the following long-term goals:

• Provide an integrated economic and environmental framework for determining feedstock supply and sustainability.
• Provide a regionally adaptive, yet nationalscale, platform for grass-based biorefining based on high-yielding feedstocks with improved environmental resilience.
• Provide a broad set of platform microorganisms, and automated tools to engineer them, to produce value-added products from plant-produced feedstocks or substrates.

Another of CABBI’s fundamental objectives is to ensure translation and commercial deployment of its research results—whether in the form of new plant cultivars; new biofuels and other biobased chemicals, lubricants, pigments, and adhesives; newly tested processes and applications; or new understanding of economic or ecological impacts.

Research Focus Areas

CABBI’s research is organized into three focus areas: Sustainability, Feedstock Production, and Conversion.

Sustainability: Improving the Environmental and Economic Bottom Line. CABBI is providing a holistic and systems-based approach to assess the economic and ecological sustainability of feedstocks, biofuels, and bioproducts developed in the Feedstock Production and Conversion research focus areas, at scales ranging from field to biorefinery to bioeconomy. Over the last 5 years, CABBI has improved fundamental understanding of ecosystem carbon, nitrogen, water, and energy fluxes in sorghum, Miscanthus, and Saccharum cropping systems and the effects of management practices and plant-microbe interactions on these ecosystem processes (Dracup et al. 2021; Tejera et al. 2019; Studt et al. 2021; Schetter et al. 2021; Hartman et al. 2022; Burnham et al. 2022; Yang, J., et al. 2022). Experimental results have been incorporated into a suite of ecosystem models: FUN-BioCROP, DayCent, and Agro-IBIS (Juice et al. 2022; Kent et al. 2020; Moore, C. E., et al. 2020; Ferin et al. 2021; Edmonds et al. 2021). The resulting improvements in cropping system representation have enabled model simulations that researchers used to generate mechanistic hypotheses for experimental testing (Hartman et al. 2022) and to assess ecosystem services production by CABBI crops across the rainfed United States.

CABBI has developed a robust platform, BioSTEAM, for conducting rapid TEA-LCA under uncertainty (Cortés-Peña et al. 2020a, b; Shi et al. 2020). BioSTEAM has been applied to characterize the viability of biodiesel and ethanol production from CABBI feedstocks and to set research and development targets for both feedstock composition and conversion technologies (Cortés-Peña et al. 2020b; Li, Y., et al. 2021; Bhagwat et al. 2021; McClelland et al. 2021). CABBI has also developed novel approaches to quantifying conventional cropland available for conversion to bioenergy crops, including (1) remote sensing of historical landuse changes (Jiang et al. 2021), (2) assessing confidence in the classification of lands as economically marginal, (3) evaluating the net social benefits of conventional food crops, and (4) adding environmental externalities to the definition of economic marginality (Khanna et al. 2021). Additionally, CABBI has developed an integrated ecosystem-economic modeling framework, called the Biofuel and Environmental Policy Analysis Model (BEPAM), which couples ecosystem models with an economic model (Ferin et al. 2021). BEPAM was used to evaluate optimal locations, feedstock mixes, biofuels and bioproducts, and the economic and environmental consequences (Yang, P., et al. 2022) of large-scale bioenergy production and to characterize the complex interactions among bioenergy policies, feedstock attributes, conversion technology, and market conditions that affect bioeconomy sustainability (Chen et al. 2021a, b).

Feedstock Production: Growing the Right Crops. CABBI is working to increase the value and resiliency of its target crops: annual sorghum (Sorghum species), temperate perennial miscanthus (Miscanthus species), and subtropical perennial energy cane (Saccharum species). Researchers have engineered the production of oils, specialty fatty acids, and other organic compounds by vegetative (nonseed) tissues in these grasses and increased biomass yield, resource use efficiency, and stress resilience. Proof-of-principle genetic crop designs have demonstrated roughly 50-fold increased oil production compared to wild-type when grown in the field, providing feedstock to the Conversion focus area and field-relevant data, materials, and infrastructure to the Sustainability focus area (Parajuli et al. 2020). CABBI has successfully engineered all three target crops and made genomic discoveries that will speed additional discovery and manipulation of natural and engineered genetic variation (Li, A., et al. 2018; Zhao et al. 2019; Eid et al. 2021; Mitros et al. 2020). These discoveries include key bioenergy traits under genetic control and improved genotypic and phenotypic methods to identify them (Dong et al. 2019, 2021; Clark et al. 2019).

Collaborations with other BRCs and DOE user facilities have produced tools and knowledge that enable targeted expression of engineered traits, paving the way for development of CABBI crops that produce oil in stem storage tissues at the end of the growing season. Methodological foundations from the Sustainability focus area provided mechanistic models, multiscale ground measurements, and remote sensing used to predict and assess hard-to-measure traits of fieldgrown CABBI crops (Varela et al. 2021, 2022). This knowledge informed the identification, creation, and testing of genetic variation, which increased productivity, thermotolerance, water use efficiency, and pollution resiliency in target crops (Li, S., et al. 2019, 2021, 2022; Kim, S., et al. 2020, 2021; Wang, S., et al. 2021; Jaikumar et al. 2021; Wang, Y., et al. 2021b). Focused collaborations with commercial partners have extended CABBI’s knowledge and impact, such as through the collection and use of the first commercial-scale Miscanthus yield monitoring data available in the United States.

Conversion: Turning Plants into High-Value Chemicals. CABBI is developing a biofoundry for biosystems design and characterizing and engineering nonmodel yeasts including Issatchenkia orientalis, Rhodosporidium toruloides, and Yarrowia lipolytica. These organisms convert plant-derived sugars and oils developed in the Feedstock Production focus area to biofuels and value-added bioproducts such as fatty alcohols, triacetic acid lactone (TAL), 3-hydroxypropanoic acid (3-HP), and citramalate. Many new tools and workflows for the design-build-testlearn (DBTL) cycle have been developed and implemented on the Illinois Biological Foundry for Advanced Biomanufacturing, an automated biofoundry platform. Examples include:

• OptRAM, an in silico strain design tool (Shen et al. 2019)
• Genetic tools for metabolic engineering of I. orientalis and R. toruloides (Schultz et al. 2019)
• Artificial enzymes with novel reactivity (Huang et al. 2020; Mirts et al. 2018)
• ECNet, a deep-learning model for protein engineering (Luo, Y., et al. 2021)
• BioAutomata, a machine learning–enabled, fully closed DBTL cycle for automated pathway engineering (HamediRad et al. 2019b)
• PlasmidMaker, a versatile, automated, and high-throughput end-to-end platform for design and construction of plasmids (Enghiad et al. 2022)

Engineering guided by metabolic modeling and metabolomics has generated I. orientalis strains capable of producing 19 g/L 3-HP, an acrylic acid precursor, and 6 g/L citramalate, a methacrylate precursor, as well as R. toruloides strains capable of producing 28 g/L TAL and 3.7 g/L fatty alcohol (Cao et al. 2022; Schultz et al. 2022). Among the four target bioproducts, TAL production and recovery is close to financial viability, according to an initial TEA-LCA study. Chemical catalysis and biocatalysis are being explored as means to upgrade the target compounds as well as fatty acids derived from oils produced in the Feedstock Production focus area. Finally, various biomass pretreatment and deconstruction methods have been developed or optimized to achieve high-efficiency recovery of sugars and oils from CABBI crops. In particular, researchers established time-domain nuclear magnetic resonance spectroscopy as a dry, inexpensive, and rapid method to quantify total lipid content and free fatty acid composition and to qualitatively determine the fractions of bound and free oil within the biomass matrix (Maitra et al. 2021).

By developing this overarching framework for a closed-loop integration of research and outcomes among the Sustainability, Feedstock Production, and Conversion research focus areas, CABBI experts are engaged in innovative research needed to achieve a sustainable bioeconomy. The framework was tested during two center-wide Feedstocks-to-Fuels pipeline collaborations that generated engineered crops for juice, oil, and bagasse production. Saccharum lines engineered to hyperaccumulate oils in their vegetative biomass and grown in Florida, Mississippi, and Illinois field trials produced almost as much oil as soybeans per unit land area, according to preliminary extrapolation of results. Agronomic performance was evaluated and triacylglycerol accumulation was analyzed by Sustainability researchers to compare the microbiome of the engineered oilcane to wild-type Saccharum. Approximately 400 kg of biomass were harvested, frozen, and shipped to the Integrated Bioprocessing Research Laboratory (IBRL) where it was bioprocessed at an industrially relevant scale. Conversion researchers used the extracted sugar and oil to generate fermentation target products, and the bagasse was hydrothermally pretreated and hydrolyzed into cellulosic sugars. The cellulosic sugars were then fermented to produce additional lipids using oleaginous yeast and the remaining oil in the bagasse was centrifuged and recovered.

Industry Partnerships

One of CABBI’s objectives is to translate its research results to commercial deployment. CABBI and the IBRL utilize an Industrial Affiliates program to engage industry in cuttingedge bioprocessing techniques and de-risk new intellectual property (IP) for transition to commercialization. The industrial affiliates get a first look at newly developed technologies in bioprocessing and bioenergy, as well as the associated IP, through an annual biotechnology showcase. IBRL also offers an annual professional biofuels course in which CABBI technologies are extensively discussed. Finally, industry representatives serve on CABBI’s strategic advisory board, bringing a corporate perspective to its research directions.

Education and Outreach

CABBI’s outreach efforts help grade-school through undergraduate students better understand bioenergy feedstock production; conversion methods to produce valuable fuels and chemicals; and economic and environmental sustainability in the field, the laboratory, and the world. Three such hands-on efforts include (1) development and implementation of the Research Internship in Sustainable Bioenergy (RISE) program for undergraduates from groups currently underrepresented in science, technology, engineering, and mathematics (STEM) research; (2) sponsorship and advising of University of Illinois undergraduates in the annual International Genetically Engineered Machine (iGEM) competition; and (3) support of the Pollen Power camp in conjunction with the Institute for Genomic Biology, an annual weeklong summer camp that provides middle school girls an opportunity to study sustainable agriculture and plant responses to climate change.

RISE participants are mentored by CABBI faculty, postdocs, and graduate students as they gain professional skills and learn about graduate school. The iGEM undergraduates conduct their own synthetic biology research project under the mentorship of CABBI faculty, postdocs, and graduate students. Members learn cutting-edge research techniques, how to work as a team, and science communication skills. At Pollen Power, small groups of girls gain first-hand experience in a range of research techniques by female graduate student mentors, such as using confocal microscopes to image fossil pollen, a technique used to reconstruct vegetation patterns in past climates.

CABBI Partners

• University of Illinois at Urbana-Champaign (lead institution)
• Archbold Biological Station (Venus, Florida)
• Boston University (Massachusetts)
• Brookhaven National Laboratory (Upton, New York)
• Colorado State University (Fort Collins)
• HudsonAlpha Institute for Biotechnology (Huntsville, Alabama)
• Iowa State University (Ames)
• Lawrence Berkeley National Laboratory (Berkeley, California)
• Lawrence Livermore National Laboratory (Livermore, California)
• Mississippi State University (Starkville)
• Princeton University (New Jersey)
• Texas A&M AgriLife Research (College Station)
• The Pennsylvania State University
• University of California—Berkeley
• University of Florida (Gainesville)
• University of Idaho (Moscow)
• University of Minnesota–Twin Cities
• University of Nebraska—Lincoln
• University of Wisconsin —Madison
• U.S. Department of Agriculture Agricultural Research Service (Houma, Louisiana; Peoria and Urbana, Illinois)
• West Virginia University (Morgantown)

CABBI Contacts

• https://cabbi.bio/

• Carl R. Woese Institute for Genomic Biology (IGB)
  1206 W. Gregory Drive, MC-195
  Urbana, IL 61801

• Phone: 217-244-1586
• Email: cabbi-bio@illinois.edu