Abstract: Methods for the fermentive production of four carbon alcohols are provided. Specifically, butanol, preferably 2-butanol is produced by the fermentive growth of a recombinant bacteria expressing a 2-butanol biosynthetic pathway. The recombinant microorganisms and methods of the invention can also be adapted to produce 2-butanone, an intermediate in the 2-butanol biosynthetic pathways disclosed herein.

Abstract: The present invention describes a process for the production of alcohol, known as second generation production, from a lignocellulosic substrate, in which a controlled quantity of furfural is produced in situ and which comprises at least the following steps: a first step for alkaline chemical pre-treatment of the substrate; a step for adjusting the pH of the substrate; then a step for enzymatic hydrolysis of said pre-treated substrate; a step for alcoholic fermentation of the hydrolysate obtained with an alcohol-producing microorganism; a step for separation/purification; and a step for acid conversion of at least one liquid fraction into furfural, said liquid fraction being obtained during one of the preceding steps; a step for mixing said furfural obtained with the pre-treated substrate during the pH adjusting step.

Abstract: Provided herein are metabolically-modified microorganisms useful for producing biofuels. More specifically, provided herein are methods of producing high alcohols including isobutanol, 1-butanol, 1-propanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 2-phenylethanol from a suitable substrate.

Abstract: Disclosed herein is a bioenergy production system with reduced carbon dioxide emissions and process wastes; including a process for producing a bioalcohol and a biogas by subjecting a biomass, such as: herbaceous and woody plants, fruit pulp, freshwater and sea algae, grains, aerobic and anaerobic sludge, saccharides, polyols and carbohydrates, to a combined process of a biosaccharification/alcohol fermentation, including a biomass pretreatment process; and a process for producing a methane biogas with a reduced level of carbon dioxide and hydrogen sulfide, via an algae cultivation process with a view to purifying the carbon dioxide and hydrogen sulfide contained in the biogas; wherein, when the algae to be cultivated is microalgae, biodiesel is produced by subjecting the harvested microalgae to a biodiesel manufacturing process while recycling the glycerol and the saccharide-containing waste produced as byproducts to the biosaccharification/alcohol fermentation process, and when the algae to be cultivated is

Abstract: The embodiments described herein pertain to cells, and methods for preparing cells, that can be used as biocatalysts by altering enzymes that compete for a substrate or product of a pathway of interest such that the targeted enzyme is sensitive to a site-specific protease, which protease is expressed but relocated in the cell to a site where it is not in contact with the targeted enzyme in the intact cell. Upon cell lysis, the protease contacts the target enzyme, which is then inactivated by protease cleavage.

Abstract: A method for producing butanol through microbial fermentation, in which the butanol product is removed during the fermentation by extraction into a water-immiscible organic extractant in the presence of at least one electrolyte at a concentration at least sufficient to increase the butanol partition coefficient relative to that in the presence of the salt concentration of the basal fermentation medium, is provided. The electrolyte may comprise a salt which dissociates in the fermentation medium, or in the aqueous phase of a biphasic fermentation medium, to form free ions. Also provided is a method and composition for recovering butanol from a fermentation medium.

Abstract: Methods of producing renewable materials may include consuming a fermentation feedstock with a fermentation organism to produce a renewable material in fermentation broth; water may then be separated from the feedstock or broth using one or more phase separations, or the renewable material may be concentrated from the feedstock or broth using one or more phase separations. Methods of producing biofuel components may include consuming a lignocellulosic or sugar fermentation feedstock with a fermentation organism to produce either ethanol or butanol in fermentation broth; cooling the feedstock or broth to solidify at least some water therein; and separating the solidified water from the feedstock or broth using a solid-liquid phase separation.

Abstract: The present invention provides various combinations of genetic modifications to a transformed host cell that provide increase conversion of carbon to a chemical product. The present invention also provides methods of fermentation and methods of making various chemical products.

Abstract: Methods for the fermentive production of four carbon alcohols are provided. Specifically, butanol, preferably 2-butanol is produced by the fermentive growth of a recombinant bacteria expressing a 2-butanol biosynthetic pathway. The recombinant microorganisms and methods of the invention can also be adapted to produce 2-butanone, an intermediate in the 2-butanol biosynthetic pathways disclosed herein.

Abstract: The present disclosure relates to an improved process of producing a fermentation product, in particular ethanol. The present disclosure relates also to the use of enzymes for improving the quality of by-products in the fermentative production process and to compositions comprising enzymes capable of degrading components in the fermented mash in the fermentation process.

Abstract: Some products such as solvents, e.g., butanol, are toxic to solvent-producing microorganisms, yet fructose metabolism can facilitate the increase of protective substrates such as triglycerides, which can protect the microorganism from the toxic effect of the product. Methods are provided for producing a product, e.g., a solvent from fructose derived from a cellulosic or lignocellulosic material. Using the methods herein, a fructose solution can be fermented to a solvent more rapidly, and with better yields, than a glucose solution.

Abstract: Provided herein are non-naturally occurring microbial organisms having a formaldehyde fixation pathway and a formate assimilation pathway, which can further include a methanol metabolic pathway, a methanol oxidation pathway, a hydrogenase and/or a carbon monoxide dehydrogenase. These microbial organisms can further include a butadiene, 1,3-butanediol, crotyl alcohol or 3-buten-2-ol pathway. Additionally provided are methods of using such microbial organisms to produce butadiene, 1,3-butanediol, crotyl alcohol or 3-buten-2-ol.

Abstract: A process for the treatment of biomass comprising subjecting biomass to microbial digestion to produce volatile fatty acids and/or solvents followed by wet oxidation to reduce biosolid volume while retaining or increasing the concentration of the volatile fatty acids and/or solvents.

Abstract: Genetically manipulated cells, lysates of such cells, systems, and methods of use thereof are provided, where one or more enzymes in a pathway of interest are genetically modified to incorporate a peptide sequence that provides for relocation of the protein, e.g., to the periplasm, so as to sequester the enzyme, and where the enzyme controls flux in the pathway of interest.

Abstract: A high flux in conversion of pyruvate to acetolactate was achieved in yeast through expression of acetolactate synthase in the cytosol in conjunction with reduction in pyruvate decarboxylase activity. Additional manipulations to improve flux to acetolactate are reduced pyruvate dehydrogenase activity and reduced glycerol-3-phosphate dehydrogenase activity. Production of compounds having acetolactate as an upstream intermediate benefit from the increased conversion of pruvate to acetolactate in the described strains.

Abstract: The invention relates, in part, to nucleic acid constructs, genetically modified host cells and methods employing such constructs and host cells to increase the production of 3-methyl-2-butenol from IPP. Thus, in some aspects, the invention provides a genetically modified host cell transformed with a nucleic acid construct encoding a fusion protein comprising a phosphatase capable of catalyzing the dephosphorylation of dimethylallyl diphosphate (DMAPP) linked to an IPP isomerase capable of converting IPP to DMAPP, wherein the nucleic acid construct is operably linked to a promoter. In some embodiments, the genetically modified host cell 5 further comprises a nucleic acid encoding a reductase that is capable of converting 3-methyl-2-butenol to 3-methyl-butanol. In some embodiments, the reductase is encoded by a nucleic acid construct introduced into the cell. In some embodiments, the IPP isomerase is a Type I isomerase. In some embodiments, the IPP isomerase is a Type II isomerase.

Abstract: Processes for starting up of anaerobic, deep tank fermentation systems to anaerobically bioconvert hydrogen and carbon monoxide in a gaseous substrate stream to oxygenated organic compounds and for steady operation of such fermentation systems. In the processes injectors use a motive liquid to introduce gas substrate as a stable gas-in liquid dispersion into the deep tank fermentation reactor where at least one of: (i) adjusting the gas to liquid flow ratio through an injector, (ii) changing the rate of liquid flow through an injector, and (iii) adjusting the carbon monoxide mole fraction in the gas feed by admixture with at least one other gas, wherein the mass transfer of carbon monoxide to an aqueous menstruum in the reactor is controlled to obtain the robust growth of the microorganism and/or continued conversion of gas substrate while maintaining the carbon monoxide concentration below that amount which is unduly adverse to the microorganism.

Abstract: The invention relates to a method for oxidizing an alkane, comprising contacting the alkane with a type alkB oxidoreductase and using a type alkB oxidoreductase to prepare a mixture of oxidation products of an alkane, wherein the ratio of carboxylic acid to alcohol in the oxidation products is preferably greater than 1:1.

Abstract: The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present disclosure generally pertains to a method of facilitating the bioconversion of glycerol by microorganisms. In one embodiment, biodiesel derived crude glycerol is purified by removing fatty acids through acid precipitation. The fatty acid-free crude glycerol is then utilized as a carbon source for the culture of microorganisms and the production of value added substances. Additionally, the unsaturated fatty acids within the biodiesel-derived crude glycerol are converted to saturated fatty acids, allowing for fermentation behavior similar to that of pure glycerol. Both the cultured microorganisms and the culture media containing the purified crude glycerol may be analyzed for crude glycerol bioconversion products. The disclosure also relates to a method of increasing product yield through the addition of a second carbon source to the microorganism culture media.

Abstract: The invention relates to the fields of industrial microbiology and alcohol production. The invention also relates to the development of a microorganism capable of producing fermentation products via an engineered pathway, and uses of the microorganism. The invention also relates to the methods to improve cell viability and productivity and the use of recycling and acid washing to increase the yield of fermentation products.

Abstract: The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Abstract: The invention relates to a method for producing a low-molecular-weight organic compound, such as acetone, butanol, and ethanol, in a fermentation process. The method contains a step of introducing a gas flow into an aqueous solution containing microorganisms producing the low-molecular-weight organic compound; a step of recovering the gas flow through a compound comprising isophoron; and optionally a step of separating the low-molecular-weight organic compound from the composition comprising isophoron.

Abstract: The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Abstract: Methods and systems for producing a biofuel using genetically modified sulfur-oxidizing and iron-reducing bacteria (SOIRB) are disclosed. In some embodiments, the methods include the following: providing a SOIRB that have been genetically modified to include a particular metabolic pathway to enable them to generate a biofuel; feeding a first source of ferric iron to the SOIRB; feeding sulfur, water, and carbon dioxide to the SOIRB; producing at least the first particular biofuel, a first source of ferrous iron, sulfate, excess ferric iron, and an SOIRB biomass; electrochemically reducing the excess ferric iron to a second source of ferrous iron; providing an iron-oxidizing bacteria that have been genetically modified to include a particular metabolic pathway to enable them to generate a second biofuel; producing at least the second biofuel, a second source of ferric iron, and an IOB biomass; and feeding the second source of ferric iron to the SOIRB.

Abstract: The invention relates generally to methods and compositions for maintaining and manipulating microbial cultures of Gram-positive bacteria. Also provided are methods for identifying quorum sensing regulatory proteins and auto-inducing peptides in Gram-positive bacteria. Also provided are methods and compositions believed to affect quorum sensing pathways of the genus Clostridium to direct or maintain enhanced butanol production of Clostridium in a desired differentiated state during sequential or continuous culture. Differentiated states include extended serial propagation, and continuous culture, for the production of butanol or other fermentation products. Further provided are methods where the concentration of butanol in peptide treated cultures of the genus Clostridium increase more rapidly and produce a substantially greater amount of butanol than in Clostridium cultures not treated with the peptide.

Abstract: The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: Yeast cells with a reduced general control response to amino acid starvation were found to have increased tolerance to butanol in the growth medium. The reduced response was engineered by genetic modification of a gene involved in the response, a GCN gene, to eliminate activity of the encoded protein. Yeast strains with an engineered butanol biosynthetic pathway and a genetic modification in a gene involved in the general control response to amino acid starvation, which have increased butanol tolerance, are useful for production of butanol.

Abstract: Integrated processes are disclosed for the conversion of coal containing mercury compounds, hydrocarbon-containing compounds, sulfur-containing compounds and nitrogen-containing compounds to chemicals in which coal is heated to remove mercury components, pyrolyzed to remove sulfur-containing and nitrogen-containing compounds and then gasified to provide syngas, and syngas is bioconverted to liquid product.

Abstract: Scalable biomaterial-based bioreactors are described. In one embodiment, the bioreactor may comprise perforated plates stacked such that the assembled bioreactor has the necessary manifolds and chambers to transport gas and liquids to a biomaterial contained within the bioreactor, and to remove the reaction products. In another embodiment, single use bioreactors are described. Methods of operating the bioreactors are also described.

Abstract: A xylan-containing feed is contacted, in the first reactor essentially operated at plug flow, with an aqueous solution of an acid at a temperature in the range from equal to or more than 140° C. to equal to or less than 210° C. to produce an intermediate product. Then, the intermediate product is contacted, in the second reactor which comprises a continuously stirred tank reactor, with an aqueous solution of an acid at a temperature in the range from more than 130° C. to equal to or less than 200° C. to produce a final product.

Abstract: An object of the present invention is to provide a soft biomass decomposition method, a production method for a target substance from soft biomass, and an enzyme or group of enzymes for decomposing soft biomass. Provided is a soft biomass decomposition method, including a step of bringing an enzyme selected from specific exocellulase, endocellulase, and processive endocellulase into contact with soft biomass such as bagasse and rice straw. Also provided is a production method for a target substance from soft biomass by incorporating the soft biomass decomposition method as a step. Further provided is an enzyme or group of enzymes for decomposing soft biomass selected from specific exocellulase, endocellulase, and processive endocellulase.

Abstract: The present invention provides methods for degrading or converting a cellulosic material using an enzyme composition in the presence of a reducing agent. The present invention also provides methods for producing a fermentation product and methods of fermenting a cellulosic material using an enzyme composition in the presence of a reducing agent.

Abstract: In an alcohol fermentation process, oil derived from biomass is hydrolyzed into an extractant available for in situ removal of a product alcohol such as butanol from a fermentation broth. The glycerides in the oil can be catalytically (e.g., enzymatically) hydrolyzed into free fatty acids, which form a fermentation product extractant having a partition coefficient for a product alcohol greater than a partition coefficient of the oil of the biomass for the product alcohol. Oil derived from a feedstock of an alcohol fermentation process can be hydrolyzed by contacting the feedstock including the oil with one or more enzymes whereby at least a portion of the oil is hydrolyzed into free fatty acids forming a fermentation product extractant, or the oil can be separated from the feedstock prior to the feedstock being fed to a fermentation vessel, and the separated oil can be contacted with the enzymes to form the fermentation product extractant.

Abstract: This invention comprises a process for the bioconversion of a fermentable carbon source to n-butanol by a microorganism, wherein the microorganism is deficient in at least one gene or protein involved in the four-carbon compounds pathway regulation to improve the four-carbon compounds pathway, particularly by inactivation of the transcriptional repressor rex.

Abstract: The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present invention relates to microorganisms and polypeptides for detoxifying aldehydes associated with industrial fermentations. In particular, a heat-stable, NADPH- and iron-dependent alcohol dehydrogenase was cloned from Thermoanaerobacter pseudethanolicus 39E and displayed activity against a number of aldehydes including inhibitory compounds that are produced during the dilute-acid pretreatment process of lignocellulosic biomass before fermentation to biofuels. Methods to use the microorganisms and polypeptides of the invention for improved conversion of bio mass to biofuel are provided as well as use of the enzyme in metabolic engineering strategies for producing longer-chain alcohols from sugars using thermophilic, fermentative microorganisms.

Abstract: Ethanol and other liquid products are produced by contacting syngas components such as CO or a mixture of CO2 and H2 with a surface of a membrane under anaerobic conditions and transferring these components into contact with a biofilm on the opposite side of the membrane. These steps provide a stable system for producing liquid products such as ethanol, butanol and other chemicals. The gas fed on the membrane's gas contact side transports through the membrane to form a biofilm of anaerobic microorganisms that converted the syngas to desired liquid products. The system can sustain production with a variety of microorganisms and membrane configurations.

Abstract: The present invention provides a method for the biological production of n-butanol at high yield from a fermentable carbon source. In one aspect of the present invention, a process for the conversion of glucose to n-butanol is achieved by the use of a recombinant organism comprising a host C. acetobutilicum transformed i) to eliminate the butyrate pathway ii) to eliminate the acetone pathway iii) to eliminate the lactate pathway and iv) to eliminate the acetate pathway. In another aspect of the present invention, the hydrogen flux is decreased and the reducing power redirected to n-butanol production by attenuating the expression of the hydrogenase gene. Optionally the n-butanol produced can be eliminated during the fermentation by gas striping and further purified by distillation.

Abstract: The invention relates to suitable candidate ADH enzymes for production of lower alkyl alcohols including isobutanol. The invention also relates to recombinant host cells that comprise such ADH enzymes and methods for producing lower alkyl alcohols in the same.

Abstract: The invention provides a microbial eukaryotic cell capable of utilizing C5 sugars, in particular xylose. Another objective of the invention is to provide an improved protein sequence to enable eukaryotic cells to degrade C5 sugars. The present invention thus provides protein comprising an amino acid sequence having at least 75% identity, preferably 80% identity, most preferably 90% identity, most highly preferably 95% identity to SEQ ID NO. 2 or SEQ ID NO. 8 and having xylose-isomerase activity in a eukaryotic cell.

Abstract: This disclosure provides a business method and system for generating sugars and recycling a non-biomass component from a waste stream. In some embodiments, a waste stream comprising cellulose and a non-biomass component is saccharified to produce glucose, followed by recovery of the glucose and non-biomass component, which may be recycled to another site associated with production of a cellulose-containing product that contains the non-biomass component. In certain scenarios, the waste stream is generated at a first location, cellulose pretreatment (if desired) and hydrolysis are conducted at a second location, and the non-biomass component is recycled to the first location or a third location. The non-biomass component may include metals, metal oxides, salts, organic compounds, inorganic compounds, oligomers, or polymers, for example.

Abstract: Fatty acids derived from biomass at a step in a fermentation process can be added to a fermentation medium comprising a recombinant microorganism that produces a product alcohol. At least one of growth rate and fermentable carbon consumption of the microorganism is greater in the presence of the fatty acids than the growth rate and the fermentable carbon consumption of the microorganism in the absence of the fatty acids. The addition of the fatty acids can increase glucose consumption, and can improve microorganism biomass production (cell growth/density) and growth rate, thereby reducing production time and increasing productivity of the fermentation process.

Abstract: When lignocellulosic biomass hydrolysate is included in fermentation medium, the broth resulting from biocatalyst production is complex with low filterability. A heat treatment was found to increase filterability, allowing efficient separation of a liquid fraction from a solid fraction, which is further processed for water recycle and syrup production.

Abstract: This invention is directed to methods for recovery of C3-C6 alcohols from dilute aqueous solutions, such as fermentation broths. Such methods provide improved volumetric productivity for the fermentation and allow recovery of the alcohol. Such methods also allow for reduced energy use in the production and drying of spent fermentation broth due to increased effective concentration of the alcohol product by the simultaneous fermentation and recovery process which increases the quantity of alcohol produced and recovered per quantity of fermentation broth dried. Thus, the invention allows for production and recovery of C3-C6 alcohols at low capital and reduced operating costs.

Abstract: Processes are described for fractionating lignocellulosic biomass into cellulose, hemicellulose, and lignin, comprising fractionating lignocellulosic biomass in the presence of a solvent for lignin (such as ethanol), a hydrolysis catalyst (such as sulfur dioxide), and water, to produce a liquor containing hemicellulose, cellulose-rich solids, and lignin; hydrolyzing the hemicellulose to produce hemicellulosic monomers; saccharifying the cellulose-rich solids to produce glucose; recovering the hemicellulosic monomers and the glucose, separately or in a combined stream, as fermentable sugars; and fermenting the fermentable sugars to a fermentation product having a higher normal boiling point than water. Process integration of mass and/or energy is disclosed in many specific embodiments. The fermentation product may include an organic acid, an alcohol, a diol, or combinations thereof.

Abstract: The present invention is related to recombinant host cells comprising: (i) at least one deletion, mutation, and/or substitution in an endogenous gene encoding a polypeptide that converts pyruvate to acetaldehyde, acetyl-phosphate, or acetyl-CoA; and (ii) a heterologous polynucleotide encoding a polypeptide having phosphoketolase activity. The present invention is also related to recombinant host cells further comprising (iii) a heterologous polynucleotide encoding a polypeptide having phosphotransacetylase activity.

Abstract: Methods of recovering butanol, and preferably increasing the rate and/or yield of its production, from the fermentation of material derived from the digestion of non-cellulosic biomass.

Abstract: Methods for producing a biofuel are provided. Also provided are biocatalysts that convert a feedstock to a biofuel.