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At least 73 records · Page 4

Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source

Abstract Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR–Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.

Biotechnology & Applied Microbiology↗

Cytochrome Nanowire XRD

Microbial metabolism plays an important role in the global cycling of carbon, nutrients, and metals. Recent discovery of microorganisms sharing energy using direct electrical connections might represent a prominent strategy by which anaerobic microorganisms interact with the diversity of environments. The purpose of the proposed research is to apply these newly developed principles of electron exchange in microbial communities to the study of biogeochemical cycling in climate and subsurface systems. Previous studies revealed that soil bacteria Geobacter sulfurreducens produce conductive pili nanofilaments that facilitate long-range electron transport to extracellular electron acceptors and other cells. This discovery has already transformed our understanding of the function of microbial communities in diverse environments, making basic contributions to microbial ecology and helping to improve practical applications such as increasing current output of microbial fuel cells and enhancing the conversion of organic waste to methane. Microbial electron exchange via pili may also contribute to methane production in terrestrial environments that are major sources of atmospheric methane. However, the mechanism of electron transport through pili is not well understood. Initial studies have suggested that pili exhibit metallic-like conductivity similar to conducting polymer polyaniline. However, these studies were limited to electrical measurements. X-ray diffraction studies have suggested that aromatic amino acids tyrosine and phenylalanine are closely packed in pili. But these studies used homology modeling to predict the pilus assembly and information about the number of monomers in each pilus assembly unit and their organization are still lacking. The central hypothesis of this proposal is aromatics in pili enable intermolecular electron delocalization due to pi-stacking that can give rise to metallic-like conductivity. By analyzing pili structure using infrared scattering-scanning near field optical microscope (IR s-SNOM) and combining with solution NMR, Focused Ion Beam (FIB and computational capabilities, this work will provide comprehensive understanding of the conduction mechanism from a structure-function perspective. The specific aims are: 1) With infrared scattering scanning near field optical microscope (IR s-SNOM), image the organization and density of pilin monomers and pH-induced conformational changes in a pilus filament. 2) With solution NMR, resolve pH-induced structural changes in the pilin monomer. 3) Using Focused Ion Beam (FIB), draw electrodes on single pili to measure their conductivity. 4) With computational modeling using the NWChem, simulate the effect of environment on the electronic properties of pili as a function of pH. The proposed work will gain the nanoscale insight into the structure of the pili, as the basis for understanding interspecies electrical communications. The improved understanding will be harnessed to accelerate bioenergy production and bioremediation using pili as well as for predictive modeling of carbon cycling in diverse environments to reach the central goals of DOE-BER to develop sustainable energy sources, regulate the contaminants in the subsurface and understand the effects of greenhouse gas emissions on biosphere. The proposed studies will provide design principles for engineering of electrical interactions among these communities by manipulating the amino acid composition of pili. Moreover, these studies will identify the forces that maintain the function of these communities in the face of environmental perturbation. Therefore, these studies will help to address the need "to incorporate process understanding of biogeochemical cycling into a scalable hierarchy of predictive capabilities" specified in EMSL's Science Themes.

59 BASIC BIOLOGICAL SCIENCES↗

CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids

Anaerobic fermentation with microbial communities (microbiomes) is an emerging platform for conversion of lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), which can be achieved by arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow faeces, goat faeces, and anaerobic digester sludge, selecting for fungal or bacterial dominated communities that convert sorghum biomass into VFAs. Subsequently we reconstructed metabolic networks across these enrichments based on recovered bacterial metagenome-assembled genomes (MAGs) and fungal isolate genomes and profiled their metabolic activity using metatranscriptomics to identify potential functional niches. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate and formate. Analysis of carbohydrate-active enzymes (CAZymes) revealed fine-scale differences between microbes that expressed unique multi-functional enzymes linking two or more CAZymes together with distinct carbohydrate binding motifs, implicating lignocellulose structure as a key driver of selection and niche differentiation. Most of these multi-functional enzymes localized complementary degradation functions together, likely conferring synergistic degradation effects within and between microbiome members. We anticipate that these findings will help inform efforts to develop synthetic microbiomes with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.

Lawson, Christopher E [University of Toronto;]↗

Current trends in waste valorization

This paper presents the scientific breakthroughs made in bioprocess engineering and microbial biotechnology for the conversion of wastes into products with added value and/or biofuels. The significant results obtained in the emerging fields of hybrid electrosynthesis, the role of enzymes in the degradation of plastics, polyhydroxyalkanoate and 5-aminolevulinic acid production, fermentation technology and the application of molecular engineering tools to bioprocess technology are highlighted.

09 BIOMASS FUELS↗

Closing the loop on plastics: Biological and hybrid routes for converting plastic waste to polyhydroxyalkanoates

Polyhydroxyalkanoate (PHA) production from plastic-derived substrates offers a promising route to mitigate plastic pollution while reducing dependence on conventional PHA feedstocks. Plastic waste represents an abundant carbon source for microbial fermentation, but efficient conversion remains limited by incomplete deconstruction, inhibitory intermediates, low carbon recovery, and challenges in process integration. Plastic-derived streams contain diverse compounds, including fatty acids, hydrocarbons, fatty alcohols, aldehydes, esters, and aromatic compounds generated during depolymerization. These intermediates can be metabolized by selected microorganisms, particularly Pseudomonas species with versatile fatty-acid and hydrocarbon pathways, as well as Cupriavidus necator and mixed microbial cultures. Unlike reviews that address plastic upcycling or PHA biosynthesis separately, this review focuses on the deconstruction–fermentation interface that governs plastic-to-PHA conversion. It consolidates current progress in plastic deconstruction, substrate conditioning, microbial metabolism, fermentation control, polymer recovery, and techno-economic and life-cycle considerations. Here, by emphasizing substrate composition, biological compatibility, plastic‑carbon recovery, and final polymer quality, the review identifies priorities for scalable and environmentally sustainable PHA production from plastic-derived substrates.

42 ENGINEERING↗

BETO 2021 Peer Review - Improving Formate Upgrading by Cupriavidus Necator 2.3.2.111

Formate can be generated by electrocatalytic reduction of CO2 and has been proposed as a soluble intermediate for the storage of carbon and energy. Biological systems capable of assimilating formate could enable conversion of formate generated from low-cost renewable energy and waste CO2 to myriad fuels and chemicals. To that end, the goal of this project is to develop the natural formatotroph Cupriavidus necator as a robust microbial chassis for efficient conversion of formate to value-added products. Using a combination of laboratory evolution and rational engineering, we have identified mutations and genetic deletions that improve its growth rate and biomass yield on formate by 1.2X. Using RNA-seq transcriptomics, we are elucidating the mechanisms that underly these improvements and anticipate this will contribute to our understanding of formate conversion. We have also engineered C. necator to convert formate to the potential polymer precursor 2-hydroxymuconate semialdehyde (2HMS) by introducing an exogenous pathway and deleting competing pathways and demonstrated production and robust growth using a pH-stat bioreactor. Final techno-economic analysis and life-cycle assessment on biological production of 2HMS from formate will enable the DOE and other stake holders to evaluate the economic and environmental impact of this project and related technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Conversion of CO 2 to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO 2 , has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. Further, the metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ..delta..phcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.

59 BASIC BIOLOGICAL SCIENCES↗

Pilot microbial electrolysis cell closes the hydrogen loop for hydrothermal wet waste conversion to jet fuel

The global shift toward net-zero emissions necessitates resource recovery from wet waste. In this study, we demonstrate the first feasibility of combining pilot-scale microbial electrolytic cells (MECs) with hydrothermal liquefaction (HTL) for simultaneous post-hydrothermal liquefaction wastewater (PHW) treatment and efficient hydrogen (H₂) production to meet biocrude upgrading requirements. Long-term single reactor operation revealed that fixed anode potential enabled rapid startup, and low catholyte pH and high salinity were effective in suppression of cathodic methanogenesis and acetogenesis – resulting in high current density of 16.6 A m –2 and 9.3 A m –2 when feeding synthetic wastewater and PHW respectively. Additionally, the anode biofilm exhibited spatial variations in response to local environmental conditions. In conclusion, onsite parallel or serial operations of multiple MECs showed good performance using actual PHW with a record-high H 2 production rate of 0.5 L L R day –1 for MEC over 10 liters scale, and the optimal chemical oxygen demand (COD)-to-H 2 yield reached 0.127 kg-H 2 per kg-COD, supporting a self-sufficient, closed-loop upgrade to jet fuel.

08 HYDROGEN↗

Rational Optimization of Microbial Processing for High Yield CO 2 -to-Isopropanol Conversion: Cooperative Research and Development Final Report, CRADA Number CRD-20-17114

This project focuses on the production of the fuel blendstock isopropanol using a CO 2 -fixing Clostridium by metabolic engineering and process optimizations. The project will initiate from a baseline isopropanol producer and pursue isopropanol production at high carbon-conversion efficiency. We will lead engineering work by in-depth pathway analyses including thermodynamics optimization, enzyme expense analysis, metabolic robustness analysis, and -omics analysis. The isopropanol production will be optimized via genome editing followed by fermentation optimizations. This project will deliver a novel microbial process that efficiently converts waste CO 2 to isopropanol at ~g/L titer level within 18-months. This project will layout a solid knowledge basis and technology platform for renewable CO 2 valorization to bio-blendstock that help achieve Co-Optima and Shell's goals.

09 BIOMASS FUELS↗

Advancing biological processing for valorization of plastic wastes

We report the useful applications of plastics are as significant as the problems associated with their disposal. Current waste management strategies are ineffective at preventing the flow of plastics into landfills, wastewater treatment, and the environment. Despite the importance of recycling technologies, most plastics are used for consumables and are discarded after limited usage. Moreover, only certain plastics are recycled, and those that are generally yield lower value products. Discovering alternative routes for valorizing plastic wastes is essential. Emerging research involves the use of biocatalysts (i.e., enzymes and microorganisms) to produce valuable products like specialty polymers, biosurfactants, and drug precursors from these feedstocks. These bioprocesses commonly integrate physio-chemical pretreatments (to generate biologically reactive intermediates) and biological upgrading (to convert intermediates to products). Herein, publications that explore plastic deconstruction technologies and bioprocesses are reviewed with an emphasis on plastic waste valorization. Understanding how microorganisms metabolize the intermediates of plastic degradation and manage their inhibitory effects is a prerequisite for engineering bioprocesses. For these heterogeneous wastes, a paradigm shift from axenic cultivation of microorganisms to cultivation of microbial consortia may benefit conversion efficiency and stress resilience. Thus, a summary is provided for metabolic pathways and constituent enzymes required to synthesize biofuels, biomaterials, and chemicals from biologically reactive intermediates. Colossal challenges associated with the use of plastics as feedstocks for direct biological processing highlight the need for integrating physical, chemical, and biological technologies.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida

Abstract With the increasing need for microbial bioproduction to replace petrochemicals, it is critical to develop a new industrial microbial workhorse that improves the conversion of lignocellulosic carbon to biofuels and bioproducts in an economically feasible manner. Pseudomonas putida KT2440 is a promising microbial host due to its capability to grow on a broad range of carbon sources and its high tolerance to xenobiotics. In this study, we engineered P. putida KT2440 to produce isoprenoids, a vast category of compounds that provide routes to many petrochemical replacements. A heterologous mevalonate (MVA) pathway was engineered to produce potential biofuels isoprenol (C 5 ) and epi-isozizaene (C 15 ) for the first time in P. putida . We compared the difference between three different isoprenoid pathways in P. putida on isoprenol production and achieved 104 mg/L of isoprenol production in a batch flask experiment through optimization of the strain. As P. putida can natively consume isoprenol, we investigated how to prevent this self-consumption. We discovered that supplementing l -glutamate in the medium can effectively prevent isoprenol consumption in P. putida and metabolomics analysis showed an insufficient energy availability and an imbalanced redox status during isoprenol degradation. We also showed that the engineered P. putida strain can produce isoprenol using aromatic substrates such as p -coumarate as the sole carbon source, and this result demonstrates that P. putida is a valuable microbial chassis for isoprenoids to achieve sustainable biofuel production from lignocellulosic biomass. Graphical Abstract

09 BIOMASS FUELS↗

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗

Analytical Modeling of Biomass Transport and Feeding Systems

The processing of biomass solids in a biorefinery consists of pretreatment, enzyme hydrolysis / concurrent fermentation of sugars to ethanol, product recovery, and drying. Sustainable operation requires a front end that transforms wet solids into a pumpable slurry. Otherwise the biorefinery will suffer unscheduled shut-downs and inefficient operation due to solids that obstruct pumps and other equipment and resist mixing in a bioreactor. Downtime in pioneer biorefineries due to interruptions from materials handling problems has been 50% or more, leading to unsustainable manufacturing processes. This work addresses new technology, predictive computational models, and definition of operational conditions that result in formation of slurries of corn stover at up to 300 g/L using low enzyme loadings (1 to 3 FPU cellulase/g) before the biomass (corn stover) enters the pretreatment step. A team of researchers from Purdue University, Idaho National Laboratory (INL), Forest Concepts, AdvanceBio, Argonne National Laboratory, and DOE BETO have combined their knowledge in agricultural and biological engineering, bioprocess engineering, mechanical engineering, chemical engineering, agricultural economics, materials engineering and enzyme and microbial technology to address the challenge of making lignocellulose flow. This team effort has resulted in the development and validation of conditions that employ low levels of commercial enzyme in an agitated bioreactor to which corn stover pellets are added resulting in formation of slurries at high solids loadings, before pretreatment. This approach overcomes challenges caused by handling of dry, particulate biomass materials at the front end of the biorefinery. The subsequent materials handling issues cause obstruction at pumps, pipes and valves. Formation of high loadings slurries with low yield stress, as reported here, significantly decreases the potential for process interruption and enhances plant operability. Key advances in the knowledge of how slurry formation occurs is reported here and in recently published journal papers. We found that pellets are needed to achieve high solids loading, and that commercial enzymes are effective in forming slurries of corn stover particles from pellets that have not been pretreated. Our work has resulted in models that predict solids behavior for formation of compressed solids and pellets that in turn facilitate slurries made of high concentrations of corn stover particles. A computational model was developed that gives mechanistic insights into properties of particles and mixing process that gives the slurry rheology needed to facilitate pumping. Hence, the corn stover may be pumped into a pretreatment reactor in place of auguring in solids against high pressure which is a root cause of interruptions at the front end of a biorefinery. Subsequent mixing in enzyme and microbial bioreactors results in conversion of lignocellulose to sugars in a biorefinery in agitated bioreactors, with flows in and out of the vessels being less likely to be interrupted due to plugging or materials handling problems. The obtained data coupled to process models, techno-economic assessment (TEA) and Life Cycle Analysis (LCA) were used to assess whether this approach is practical. These results are based on a foundation of laboratory characterization and pilot runs. The NREL biochemical sugar model was utilized to carry out techno-economic analysis of enzyme catalyzed liquefaction followed by enzyme hydrolysis. The minimum sugar selling price was between 17.5 and 18.3 ¢/pound or about the same as calculated by the NREL model for dilute acid pretreatment followed by enzyme hydrolysis. Life cycle analysis (LCA) based on Argonne’s Greet Model showed the enzyme catalyzed route had the lowest greenhouse gas emissions of the three combinations studied (i.e., enzyme, enzyme mimetic, and enzyme + mimetic combined). GHG emissions for enzyme-based corn stover liquefaction step, alone, were about 21 g CO 2 -equivalent/kg of liquefied slurry. We believe this approach will further enhance operability of a pioneer biorefinery, and bring large-scale conversion of lignocellulosic biomass to low carbon footprint biofuels closer to implementation.

09 BIOMASS FUELS↗

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗

Resilient Crop Production for the Bioeconomy: Frontier Science for the Bioeconomy Workshop Series

A bioeconomy based on energy, chemicals, and bioproducts derived from nonfood crops promotes U.S. prosperity, energy independence, and national security. Crop productivity (i.e., yield) affects profitability for farmers, whereas biomass and seed oil quality affects profitability for biorefineries through the conversion efficiency of feedstock crops into energy, chemicals, and bioproducts. Scientific breakthroughs in plant genetics and genomics, ecological processes, bioprocessing, microbial engineering and design, and conversion technologies have improved the potential market viability of products derived from nonfood crops specifically cultivated as biomass and seed oil feedstocks. Improving understanding of a plant’s complex responses to withstand or recover from stress is crucial to maintaining feedstock yield and quality, particularly in challenging production zones. Stress may be related to biotic or abiotic (i.e., nonliving) environmental conditions that negatively affect plant growth, development, and productivity. Research and development to enhance the environmental resilience of feedstock crops will enable improved production by minimizing losses during stress and improving production on currently economically nonviable marginal lands.

09 BIOMASS FUELS↗