Abstract: Embodiments of the present disclosure relate to a process for producing downstream products, such as fermentable sugars and end products, from a starch substrate by saccharification and/or fermentation. The saccharification is effectively catalyzed by a glucoamylase at a pH in the range of 5.0 to 8.0. At a pH of 6.0 or above, the glucoamylase possesses at least 50% activity relative to its maximum activity. The saccharification and fermentation may be performed as a simultaneous saccharification and fermentation (SSF) process.

Abstract: A method for preparing a target chemical derivable from cellulosic biomass, involving detoxification of spent hydrolysate is provided. The method comprises the steps of providing cellulosic biomass, subjecting the cellulosic biomass to aqueous pretreatment, aqueous hydrolysis, and fermentation under conditions in which at least a part of the fermentable sugars are fermented into a primary target chemical, separating the primary target chemical from the fermented hydrolysate to provide a spent hydrolysate comprising inhibitory substances and detoxifying the spent hydrolysate by decreasing the concentration of at least one of the inhibitory substances using a detoxification biocatalyst selected from the group consisting of wild type, mutant and recombinant filamentous fungi and recirculating at least a part of the detoxified spent hydrolysate, optionally after further purification.

Abstract: Constructs, vectors and cyanobacteria for the synthesis of fatty alcohols, and methods for producing fatty alcohols in cyanobacteria is disclosed.

Abstract: This invention is a process for managing the gas flow through a plurality of bioconversion modules that provide a gas liquid interface. The conversion modules provide the gas liquid interface across an activated surface that converts at least some of the gas components into desired liquid products. Arrangement of the modules and control of gas flow in accordance with this invention enhances the utilization of the gas and the production of desired liquid products by adjusting the flow area to compensate for changes in the volume of the feed gas. Improved control of the gas velocity through the bioconversion modules eliminates problems of liquid condensation and flow maldistribution. The process may sequence the modules to mitigate time variation in microorganism activity and incorporate additional periodic process steps.

Abstract: The present disclosure provides methods useful for producing fatty alcohol compositions from recombinant host cells. The disclosure further provides variant fatty acyl-CoA reductase (FAR) enzymes, polynucleotides encoding the variant FAR enzymes, and vectors and host cells comprising the same.

Abstract: A stable method for producing liquid products such as ethanol, propanol, butanol and other chemicals from syngas components that contacts CO or a mixture of CO2 and H2 with a highly porous side of an asymmetric membrane under anaerobic conditions and transfers these components into contact with microorganisms contained within bio-pores of the membrane. A liquid contacting side of the membrane utilizes a dense layer to control hydration of the bio-pores with a liquid phase. The gas feed directly contacts the microorganisms in the bio-pores and maximizes their utilization of the syngas. Metabolic products produced by the microorganisms leave the membrane through the side opposite the entering syngas. This method establishes a unitary direction across the membrane for the supply of the primary feed source to the microorganisms and the withdrawal of metabolically produced products. The feed and product flow improves productivity and performance of the microorganism and the membrane.

Abstract: A process for conversion of syngas to liquid products that serve as surface acting agents uses the gas stream at a relatively low pressure to eliminate the use of a compressor. The process uses a liquid stream as the primary energy input to a gas injector that intensely mixes gas and the liquid with reduced compression costs while the presence of the liquid product maintains the gas-liquid dispersion as it flows downward to build a static pressure head. The process lowers the required gas pressure by adjusting the elevation of the gas injector such that a conduit receives the gas-liquid dispersion from the outlet of the injector and confines it as it travels downward to enter the bottom of a column of liquid. The liquid product provides a surface acting agent that prolongs the creation and duration of microbubbles in the gas-liquid dispersion.

Abstract: In an alcohol fermentation process, oil derived from biomass is chemically converted 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 chemically converted into a reaction product, such as fatty acids, fatty alcohols, fatty amides, fatty acid methyl esters, fatty acid glycol esters, and hydroxylated triglycerides, and mixtures thereof, which forms 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 chemically converting into the fermentation product extractant.

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: The invention provides for a novel type of biofuel; a method for cleaving anchors from photosynthetic organisms; and a method for producing biofuels using photosynthetic organisms, the method comprising identifying photosynthesis co-factors and their anchors in the organisms; modifying the organisms to increase production of the anchors; accumulating biomass of the organisms in growth media; and harvesting the anchors.

Abstract: The present invention provides methods for a robust production of isoprenoids via one or more biosynthetic pathways. The invention also provides nucleic acids, enzymes, expression vectors, and genetically modified host cells for carrying out the subject methods. The invention also provides fermentation methods for high productivity of isoprenoids from genetically modified host cells.

Abstract: The subject invention provides materials and methods wherein unique and advantageous combinations of gene mutations are used to direct carbon flow from sugars to a single product. The techniques of the subject invention can be used to obtain products from native pathways as well as from recombinant pathways. In preferred embodiments, the subject invention provides new materials and methods for the efficient production of acetate and pyruvic acid.

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: Genetically engineered cells and microorganisms are provided that produce fatty alcohols from the fatty acid biosynthetic pathway, as well as methods of their use.

Abstract: The present disclosure is generally directed to process of gasification of carbonaceous materials to produce synthesis gas or syngas. The present disclosure provides improved methods of gasification comprising: adding one or more carbonaceous materials, adding a molecular oxygen-containing gas, adding a methane-containing gas and optionally adding water or steam into said gasifier. This disclosure is also directed to process of production of one or more alcohols from said syngas via fermentation or digestion in the presence of at least one microorganism.

Abstract: Compositions and methods for producing fatty acid derivatives using recombinant microorganisms are described herein.

Abstract: The present disclosure is generally directed to process of gasification of carbonaceous materials to produce synthesis gas or syngas. The present disclosure provides improved methods of gasification comprising: adding one or more carbonaceous materials, adding a molecular oxygen-containing gas, adding carbon dioxide gas and optionally adding water into said gasifier. This disclosure is also directed to process of production of one or more alcohols from said syngas via fermentation or digestion in the presence of at least one microorganism.

Abstract: Cytochrome P450 BM-3 from Bacillus megaterium was engineered using a combination of directed evolution and site-directed mutagenesis to hydroxylate linear alkanes regio- and enantioselectively using atmospheric dioxygen as an oxidant. Mutant 9-10A-A328V hydroxylates octane primarily at the 2-position to form S-2-octanol (40% ee). Another mutant, 1-12G, hydroxylates alkanes larger than hexane primarily at the 2-position, but forms R-2-alcohols (40-55% ee). These biocatalysts are highly active for alkane substrates and support thousands of product turnovers. These regio- and enantio-selectivities are retained in whole-cell biotransformations with E. coli, where the engineered P450s can be expressed at high levels and the expensive cofactor is supplied endogenously.

Abstract: Fibrous materials, compositions that include fibrous materials, and uses of the fibrous materials and compositions are disclosed. For example, the fibrous materials can be operated on by a microorganism to produce ethanol or a by-product, such as a protein or lignin.

Abstract: This invention provides systems and methods for the increased production of ethanol and other chemical compounds by recombinant Clostridium species whereby the recombinant species are genetically-engineered to disrupt lactate dehydrogenase activity and to hydrolyze and ferment carbonaceous biomass and synthesize compounds of commercial value without production of lactic acid.

Abstract: Microorganisms for the production of high-value chemicals from free fatty acids are provided. The microorganisms comprise genetic mutations that alter fatty acid metabolism. The genetic mutations include a mutation or deletion of a fadR gene in which the FadR enzyme activity is partially or substantially eliminated and a mutation in an atoC gene that provides overexpression of the microorganism's ato operon. Methods of using the microorganisms to produce high-value chemicals are also provided. The high-value chemicals include ethanol, methyl acetate, succinate, gamma-butyrolactone, 1,4-butanediol, acetone, iso-propanol, butyrate, butanol, mevalonate, propionate, ethanolamine and 1,2-propanediol.

Abstract: There is disclosed a method of producing isobutanol. In an embodiment, the method includes providing a microorganism transformed with an isobutanol producing pathway containing at least one exogenous gene. The microorganism is selected to produce isobutanol from a carbon source at a yield of at least 10 percent theoretical. The method includes cultivating the microorganism in a culture medium containing a feedstock providing the carbon source, until isobutanol is produced. The method includes recovering the isobutanol. In one embodiment, the microorganism is a yeast with a Crabtree-negative phenotype. In another embodiment, the microorganism is a yeast microorganism with a Crabtree-positive phenotype. There is disclosed a microorganism for producing isobutanol. In an embodiment, the microorganism includes an isobutanol producing pathway containing at least one exogenous gene, and is selected to produce a recoverable quantity of isobutanol from a carbon source at a yield of at least 10 percent theoretical.

Abstract: A process for producing a fermentation product from a lignocellulose-containing material includes pre-treating the lignocellulose-containing material; introducing chitosan or a chitosan-like polymer to the pre-treated lignocellulose-containing material; exposing the pre-treated lignocellulose-containing material to an effective amount of a hydrolyzing enzyme; and fermenting with a fermenting organism to produce a fermentation product.

Abstract: Disclosed herein are methods of degrading plant biomass, and microorganisms and polypeptides used in such methods, hi certain embodiments, the methods include growing Anaerocellum thermophilum on a substrate that comprises plant biomass under conditions effective for the A. thermophilum to convert at least a portion of the plant biomass to a water soluble product or a water insoluble product, hi some cases, the method can further include one or more steps to further process the water soluble product or a water insoluble product to produce, for example, a biofuel or commodity chemical. In another aspect, microorganisms that include at least one A. thermophilum plant biomass utilization polynucleotide are disclosed. Also disclosed are methods of transferring one or more A. thermophilum plant biomass utilization polynucleotides to a recipient microorganism. A. thermophilum plant biomass utilization polynucleotides and polypeptides encoded by such polynucleotides are also disclosed.

Abstract: The present invention relates to enzymic processes for preparing S-butan-2-ol; and to enzymes for carrying out said processes; to nucleic acid sequences coding for said enzymes, to expression cassettes, vectors and recombinant hosts containing said nucleic acid sequences.

Abstract: A process of producing an organic compound and/or an intermediary compound as defined herein by feeding carbon dioxide to a culture of a cyanobacterial cell and subjecting the culture to light, wherein the cell is capable of expressing a nucleic acid molecule, wherein the expression of the nucleic acid molecule confer on the cell the ability to convert a glycolytic intermediate into the organic compound and/or into the intermediary compound and wherein the nucleic acid molecule is under the control of a regulatory system which responds to a change in the concentration of a nutrient in the culture.

Abstract: Provided is a method for producing alcohol or hydrogen gas comprising culturing alcohol-producing microorganisms in a waste fermented solution generated from the bioethanol production process. Glycerol included in the waste fermented solution generated from the bioethanol production process is converted by the microorganisms to butanol under an anaerobic condition. Since the waste fermented solution generated from the bioethanol production process can be utilized as a source of a biofuel, environmental and energy problems can be solved at once.

Abstract: The invention provides a non-naturally occurring microbial organism having n-propanol and isopropanol pathways, 1,4-butanediol (14-BDO) and isopropanol pathways, 1,3-butanediol (13-BDO) and isopropanol pathways or methylacrylic acid (MAA) and isopropanolpathways. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in each of the respective n-propanol, 14-BDO, 13-BDO or MAA and isopropanol pathways. The invention additionally provides a method for co-producing n-propanol and isopropanol, 14-BDO and isopropanol, 13-BDO and isopropanol or MAA and isopropanol. The method can include culturing an n-propanol and an isopropanol co-producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an n-propanol, an isopropanol, a 14-BDO, a 13-BDO and/or a MAA pathway enzyme in a sufficient amount to produce each of the respective products, under conditions and for a sufficient period of time to produce each of the respective products.

Abstract: The invention provides a biological method of producing isoprenoids.

Abstract: The invention relates to processes and biocatalysts for producing ethanol and other useful products from biomass and/or other materials. Initial processing of lignocellulosic biomass frequently yields methylglucuronoxylose (MeGAX) and related products which are resistant to further processing by common biocatalysts. Strains of Enterobacter asburiae are shown to be useful in bioprocessing of MeGAX and other materials into useful bioproducts such as ethanol, acetate, lactate, and many others. Genetic engineering may be used to enhance production of desired bioproducts.

Abstract: Methods for the fermentative production of four carbon alcohols is provided. Specifically, butanol, preferably isobutanol is produced by the fermentative growth of a recombinant bacterium expressing an isobutanol biosynthetic pathway.

Abstract: This invention provides systems and methods for the production of compounds by C. phytofermentans. C. phytofermentans is genetically-engineered for hydrolysis and fermentation of carbonaceous biomass to synthesize compounds of commercial value.

Abstract: A stable system for producing liquid products such as ethanol, butanol and other chemicals from syngas components contacts CO or a mixture of CO2 and H2 with a hydrophilic membrane under anaerobic conditions and transfers these components into contact with microorganisms contained as a biofilm on the membrane. Maintaining the microorganisms as a biolayer on the surface of the membrane facilitates cleaning of the membrane surface that retains the biofilm. In addition the shell gas space that surrounds the membranes may be flooded to reduce or remove the biofilm. Agitation of the liquid, by for example the bubbling of gas in the surrounding shell space, can fully or partially remove the biofilm from the membrane.

Abstract: The invention provides for a method for producing a 5-carbon alcohol in a genetically modified host cell. In one embodiment, the method comprises culturing a genetically modified host cell which expresses a first enzyme capable of catalyzing the dephosphorylation of an isopentenyl pyrophosphate (IPP) or dimethylallyl diphosphate (DMAPP), such as a Bacillus subtilis phosphatase (YhfR), under a suitable condition so that 5-carbon alcohol is 3-methyl-2-buten-1-ol and/or 3-methyl-3-buten-1-ol is produced. Optionally, the host cell may further comprise a second enzyme capable of reducing a 3-methyl-2-buten-1-ol to 3-methyl-butan-1-ol, such as a reductase.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently convert carbon dioxide and light into n-alkanes, and in particular the use of such organisms for the commercial production of n-alkanes and related molecules.

Abstract: The invention provides a process for the production of an alcohol which comprises cleaving polysaccharides in a cellulosic material in an aqueous medium at a temperature of at least 45° C. using a thermophilic microorganism to yield fermentable sugars, fermenting an aqueous solution of said sugars at a temperature of at least 45° C. with a thermophilic microorganism to yield an alcohol or an alkanoate, if necessary reducing said alkanoate to yield an alcohol, and removing said alcohol from said aqueous solution.

Abstract: The invention provides a non-naturally occurring microbial organism having at least one exogenous gene insertion and/or one or more gene disruptions that confer production of primary alcohols. A method for producing long chain alcohols includes culturing these non-naturally occurring microbial organisms.

Abstract: The present invention provides methods of a process (SOLWASFUEL system) for producing biofuel and bioenergy products using, as starting raw material, home and municipal organic solid waste, including recalcitrant lignocellulosic materials of paper, cardboards, organic plastics, cellulose plants, and food waste. In accordance with the invention, home and municipal solid waste, can serve as a carbon source to support the metabolism of synthetic microorganisms to produce biofuels and bioenergy products.

Abstract: A method for the production water insoluble reactive lignin having low sulfur content and lignosulfonates from lignocellulosic material in a batch or continuous process. Lignocellulosic material is fractionated to produce water insoluble native lignin and lignosulfonates in various ratios, while preserving the cellulose and hydrolyzed hemicelluloses using water, ethanol and sulfur dioxide.

Abstract: The present disclosure relates generally to methods for processing a feedstock. Specifically, methods are provided for processing a feedstock by mixing the feedstock with an additive organism that comprises one or more transgenes coding for one or more enzymes. The expressed enzymes may be capable of breaking down cellulosic and lignocellulosic materials and converting them to a biofuel.

Abstract: A transformant capable of producing isopropanol which is constructed by transferring the following genes (a) to (d) into a coryneform bacterium: (a) an exogenous gene which encodes an enzyme having acetyl-CoA acetyltransferase activity; (b) an exogenous gene which encodes an enzyme having acetoacetyl CoA: acetate CoA-transferase activity; (c) an exogenous gene which encodes an enzyme having acetoacetate decarboxylase activity; and (d) an exogenous gene which encodes an enzyme having isopropanol dehydrogenase activity.

Abstract: The present invention relates to novel xylose-fermenting yeast strains (for example, yeast of the genus Saccharomyces, e.g., S. cerevisiae) with an enhanced ability to ferment the xylose (and/or another pentose sugar) present in a lignocellulosic hydrolysate to a fermentation product(s) (for example, an alcohol (e.g., ethanol) or a sugar alcohol (e.g., xylitol)).

Abstract: This invention describes genes, metabolic pathways, microbial strains and methods to produce 2,6-dimethyloctane as an advanced biofuel from renewable feedstocks.

Abstract: A method of producing a low molecular weight organic compound (e.g. a plant or bacteria secondary metabolite) in increased yields involving use of a microorganism cell, which comprises a gene involved in the biosynthesis pathway leading to a low molecular weight organic aglycon compound and a glycosyltransferase gene capable of glycosylating the produced aglycon.

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: The invention relates to polypeptides having glucanase, e.g., endoglucanase, mannanase, xylanase activity or a combination of these activities, and polynucleotides encoding them. In one aspect, the glucanase activity is an endoglucanase activity (e.g., endo-1,4-beta-D-glucan 4-glucano hydrolase activity) and comprises hydrolysis of 1,4-beta-D-glycosidic linkages in cellulose, cellulose derivatives (e.g., carboxy methyl cellulose and hydroxy ethyl cellulose) lichenin, beta-1,4 bonds in mixed beta-1,3 glucans, such as cereal beta-D-glucans or xyloglucans and other plant material containing cellulosic parts. In addition, methods of designing new enzymes and methods of use thereof are also provided. In alternative aspects, the new glucanases e.g., endoglucanases, mannanases, xylanases have increased activity and stability, including thermotolerance or thermostability, at increased or decreased pHs and temperatures.

Abstract: Ethanol and other liquid products are produced from biomass using gasification of the biomass to produce a syngas containing CO2, CO, H2 and sulfur or sulfur compounds that passes the syngas to a fermentation step for the conversion of the CO and CO2 and H2 to ethanol. Sulfur and sulfur compounds in the syngas are used to satisfy sulfur demanded by bacteria in the fermentation step. A sulfur control additive is added to the gasification to control syngas sulfur and sulfur compounds at a desired concentration to meet bacteria sulfur demand.

Abstract: A photocatalytic method for the hydroxylation of alkanes involving the use of a Cytochrome P450 class of enzyme as a catalyst which is activated by exposure to a pulsed blue light emitted from a light emitting diode (LED) at 450 nm±25 nm.

Abstract: A stable system for producing liquid products such as ethanol, butanol and other chemicals from syngas components contacts CO or a mixture of CO2 and H2 with a hydrophilic membrane under anaerobic conditions and transfers these components into contact with microorganisms contained as a biofilm on the membrane. Maintaining the microorganisms as a biolayer on the surface of the membrane facilitates cleaning of the membrane surface that retains the biofilm. In addition the shell gas space that surrounds the membranes may be flooded to reduce or remove the biofilm. Agitation of the liquid, by for example the bubbling of gas in the surrounding shell space, can fully or partially remove the biofilm from the membrane.

Abstract: The invention provides a method to decrease emission of carbon dioxide from combustion of fossil fuels or other hydrocarbons and to enhance the efficiency of methane production from anaerobic biodigesters. The invention involves feeding carbon dioxide from the exhaust gas of hydrocarbon fuel combustion to an anaerobic biodigester where biomass is anaerobically fermented to produce methane. Carbon dioxide is an electron acceptor for anaerobic fermentation, and thus some of the carbon dioxide is reduced to methane, which can again be used for fuel. In this way, at least a portion of the exhaust gas CO2 is recycled to form fuel methane instead of being released into the atmosphere. Thus, the net CO2 emission from burning a given amount of fossil fuel is decreased. Adding carbon dioxide to an anaerobic fermentation also increases the efficiency and amount of methane production in the fermentation.