BioCompoundML: A General Biofuel Property Screening Tool for Biological Molecules Using Random Forest Classifiers
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Background: The chemoautotrophic bacterium Ralstonia eutropha can utilize H 2 /CO 2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO 2 , little work has been done to develop genetic part libraries to enable such endeavors. Results: We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5' mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters P BAD , T7, P xyls/PM , P lacUV5 , and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. Conclusion: We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.
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PETRO Project: Chromatin will engineer sweet sorghum—a plant that naturally produces large quantities of sugar and requires little water—to accumulate the fuel precursor farnesene, a molecule that can be blended into diesel fuel. Chromatin’s proprietary technology enables the introduction of a completely novel biosynthetic process into the plant to produce farnesene, enabling sorghum to accumulate up to 20% of its weight as fuel. Chromatin will also introduce a trait to improve biomass yields in sorghum. The farnesene will accumulate in the sorghum plants—similar to the way in which it currently stores sugar—and can be extracted and converted into a type of diesel fuel using low-cost, conventional methods. Sorghum can be easily grown and harvested in many climates with low input of water or fertilizer, and is already planted on an agricultural scale. The technology will be demonstrated in a model plant, guayule, before being used in sorghum.
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Renewable fuels can be more environmentally friendly than conventional fuels and can be produced locally, supporting energy independence. Liquid renewable fuels are of special interest due to their high energy density. Algae are a promising prospective feedstock for low carbon intensity liquid biofuels, due to their high productivity and potential for high lipid or carbohydrate content. Their ability to grow on wastewater and waste nutrients and on non-arable land are cost and sustainability advantages. The organic matter content of wastewater promotes mixotrophic and/or heterotrophic growth of both algae and bacteria, boosting biomass productivity further. However, economic and technologic challenges persist that prevent the scale-up of algal biofuels to commercial relevance. These challenges include algal harvesting, drying, dewatering, and the conversion of algal biomass to usable fuels (Hannon et al 2010, Dunlap and Shaw 2009, Pienkos et al. 2009). The US Department of Energy (DOE) Bioenergy Technologies Office (BETO) supports research to overcome these challenges and outlines the research and development goals for algal biofuels in their Multi-Year Program Plan (MYPP). The long-term goals of the MYPP for algal biofuels research are briefly as follows: develop the domestic ability to produce algal biofuels at a scale of 5 billion gallons per year (BGY) by 2030 and demonstrate technologies that produce biofuel intermediates from algae at a cost of $3/gallon of gasoline equivalent (GGE) by 2022 (BETO MYPP 2016). This research reported herein was funded to investigate methods of meeting an intermediate milestone of 2,500 gallons of biofuel intermediate per acre per year for a non-integrated process by improving algal productivity, harvesting efficiency, and conversion to biofuel intermediates. Use of wastewater and wastewater nutrients was a key distinguishing characteristic of this project. In pursuit of 2,500 gallons of biofuel intermediate (BFI) per acre per year, California Polytechnic State University, San Luis Obispo (Cal Poly) sought to develop the capability to produce biofuel intermediates from microalgae grown on municipal wastewater at a 20-acre algae-based wastewater treatment facility in Delhi, California (37.43° N), which includes 7 acres of raceway ponds. Coupling algal biofuel production with wastewater treatment capitalizes on the abundant waste nutrients and carbon present in wastewater and reduces use of clean water in algal biorefinery systems. In this research, the performance of the full-scale wastewater treatment plant was characterized by measuring productivity, wastewater treatment performance, hydraulic characteristics, and energy consumption. Nine 1,000-L pilot raceways with CO2 addition were used in experiments to maximize productivity. Low-cost, energy-efficient algae bioflocculation and settling were monitored. Population genetics were monitored in an attempt to correlate taxa with superior productivity and/or settling. Algae-bacterial biomass was converted to biofuel intermediates via bench-scale hydrothermal liquefaction (HTL), and the resulting fuel quality was characterized. To develop rapid strain screening capabilities, a climate simulating photobioreactor (“LEAPS”) was developed and validated against outdoor raceways. A techno-economic analysis (TEA) and a lifecycle assessment (LCA) were performed to model process economics and sustainability. The major outcomes of this research included demonstration of 33 g/m2-day annual average algal-bacterial productivity in pilot raceways, and a biofuel intermediate yield of 0.35 g intermediate/g algae biomass via HTL, for a yield of 4,100 gallons BFI per acre per year, assuming a 90% harvest efficiency and ignoring other minor losses. This exceeded the project goal of 2,500 gallons of BFI per acre per year and nearly met the 2030 program goal, highlighting the promise of integrating wastewater treatment and biofuels production. The biocrude BFI produced by the process is refined to diesel and naphtha fuels. These fuels are normalized to the energy content of gasoline (gallons gasoline equivalent, GGE, for comparison to other fuels). Results from the TEA of the this complete “well-to-wheel” process demonstrated that, at a 400-ha scale, a minimum fuel selling price (MFSP) of $12.55/GGE, which could be decreased 57% to $7.14/GGE when including revenue from coupling the biofuel production with the co-products of wastewater treatment services and low carbon fuel credits from California and Federal programs. Due mainly to the high capital costs of thickener centrifuges and hydrothermal processing equipment, the fuel cost is sensitive to scale, with significantly lower costs expected for larger farms. In this research project, significant advances were made in improving raceway algal productivity and fuel production from algae biomass, while also improving process economics. These outcomes brought the algal biofuel technology closer to being a sustainable and marketable process. The remainder of this executive summary is organized into the following six primary project tasks: (1) to optimize biomass productivity for a selected strain at Delhi, (2) to maximize algal productivity and harvesting efficiency in Delhi pilot ponds, (3) a full-scale raceway hydraulic characterization, (4) biomass processing to biofuel intermediates, and (5) scale-up engineering analysis, modeling, and planning.
This interdisciplinary research program at Michigan State University, in collaboration with Ford Motor Company, has explored the application of tailored or designed biofuels for enhanced vehicle performance and reduced emissions. The project has included a broad range of experimental research, from chemical and biological formation of advanced biofuel components to multicylinder engine testing of blended biofuels to determine engine performance parameters. In addition, the project included computation modeling of biofuel physical and combustion properties, and simulation of advanced combustion modes in model engines and in single cylinder engines. Formation of advanced biofuel components included the fermentation of five-carbon and six-carbon sugars to n-butanol and to butyric acid, two four-carbon building blocks. Chemical transformations include the esterification of the butyric acid produced to make butyrate esters, and the esterification of succinic acid with n-butanol to make dibutyl succinate (DBS) as attractive biofuel components. The conversion of standard biodiesel, made from canola or soy oil, from the methyl ester to the butyl ester (which has better fuel properties), and the ozonolysis of biodiesel and the raw oil to produce nonanoate fuel components were also examined in detail. Physical and combustion properties of these advanced biofuel components were determined during the project. Physical properties such as vapor pressure, heat of evaporation, density, and surface tension, and low temperature properties of cloud point and cold filter plugging point were examined for pure components and for blends of components with biodiesel and standard petroleum diesel. Combustion properties, particularly emission delay that is the key parameter in compression ignition engines, was measured in the MSU Rapid Compression Machine (RCM), an apparatus that was designed and constructed during the project simulating the compression stroke of an internal combustion engine under highly instrumented conditions. Simulation of and experimentation on combustion in single and multicylinder engines was carried out in detail throughout the project. The combustion behavior of biofuel blends neat and in petroleum were characterized in the MSU optical engine, in part to validate results obtained in the RCM and to provide data for comparison with simulations. Simulation of in- cylinder, low-temperature combustion included development of an extensive fuel injection model that included fuel spray breakup, evaporation, and ignition, along with prediction of cylinder temperature, pressure, and work produced. Single cylinder and multicylinder engine tests under advanced low-temperature combustion conditions conducted at Ford Motor Company validated experimental and simulation results obtained in the MSU engine and in MSU simulations. Single cylinder engine tests of an advanced biofuel containing biodiesel and dibutyl succinate, carried out under low-temperature combustion conditions, showed similar power generation and gas-phase emissions (CO, HC, NOx), but a reduction in particulates of as much as 60% relative to neat biodiesel and 95% relative to petroleum diesel at the same operating conditions. This remarkable finding suggests that biofuels may be able to play a role in eliminating the need for particulate removal systems in diesel vehicles. The multicylinder engine tests at Ford, carried out using butyl nonanoate as an advanced biofuel, also gave promising results, showing a strong decline in particulate emissions and simultaneously a modest decrease in NOx emissions relative to standard petroleum diesel at the same conditions. In summary, this project has shown that advanced biofuels and their blends are capable of maintaining performance while reducing emissions, particularly particulates (soot), in 3 compression ignition engines. The interdisciplinary nature of biofuel production and testing has identified fuel properties that are capable of producing such performance, thus providing direction for the implementation of renewable fuels for U.S. transportation. The testing and simulation studies have deepened our understanding of combustion 1) by advancing the rigor with which simulations can be carried out and 2) by illustrating that differences in biofuel and petroleum fuel properties can be used to predict differences in combustion behavior in engines. The future viability of biofuels for compression ignition (diesel) engines is now subject to economic (cost) uncertainty more so than to technical barriers, as the advanced biofuel blends developed here can improve cold-weather fuel properties, provide similar engine performance, and reduce emissions.