Abstract: The present invention relates to the production of biofuels by utilizing efficient biomass digestion and fermentation by a new thermophilic microorganism generated after fusion of two different bacteria Clostridium thermocellum and C. acetobutylicum and properly mutating the fused bacteria to produce biofuels and other economically important chemicals in a single vessel from lignocellulosic derived renewable biomass. All the necessary biochemical digestions and fermentation are carried out by this single thermophilic microorganism in one single vessel eliminating the need for multiple step digestion and fermentation processes, requiring multiple chambers. It also significantly reduces the rate limiting steps where increasing accumulation of alcohol, butanol and other substances become toxic to the very bacteria that produce these biofuels. The single vessel is incubated at high temperatures (45° C. or above) to eliminate the need for periodic stoppage and restarting of the process.

Abstract: The present invention in its various embodiments is directed to methods for preparing a renewable jet fuel blendstock, and blendstocks prepared by such methods, comprising fermenting a biomass-derived feedstock to form one or more C2—C6 alcohols such as isobutanol, catalytically dehydrate and oligomerize the alcohols to form higher molecular weight olefins (e.g., C8—C16 olefins), hydrogenating at least a portion of the higher molecular weight olefins to form a renewable jet fuel blendstock comprising C12 and C16 alkanes which meet or exceed the requirements of ASTM D7566-10a for hydroprocessed synthesized paraffinic kerosene (SPK).

Abstract: A group of bacterial dihydroxy-acid dehydratases having a [2Fe-2S] cluster was discovered. Bacterial [2Fe-2S] DHADs were expressed as heterologous proteins in bacteria and yeast cells, providing DHAD activity for conversion of 2,3-dihydroxyisovalerate to ?-ketoisovalerate or 2,3-dihydroxymethylvalerate to ?-ketomethylvalerate. Isobutanol and other compounds may be synthesized in pathways that include bacterial [2Fe-2S] DHAD activity.

Abstract: The present invention relates to enzyme compositions for high temperature saccharification of cellulosic material and to uses thereof.

Abstract: Provided herein are polypeptides having ketol-aid reductoisomerase activity as well as microbial host cells comprising such polypeptides. Polypeptides provided herein may be used in biosynthetic pathways, including, but not limited to, isobutanol biosynthetic pathways.

Abstract: Processes are disclosed for preparing microorganism concentrates from fermentation broth containing a free suspension of the microorganisms which is used for the anaerobic conversion of syngas to oxygenated organic compound. The processes involve the use of processing steps and the presence of certain additives to enhance the ability of the microorganism concentrate to be stored for extended periods and reactivated.

Abstract: Bacteria that are not natural butanol producers were found to have increased tolerance to butanol when the membrane content of unsaturated trans fatty acids was increased. Feeding cells with unsaturated trans fatty acids increased their concentration in the membrane, which may also be accomplished by expressing a fatty acid cistrans isomerase.

Abstract: A method to recover and harvest nutrients from a liquid stream by incorporating them into microorganisms grown in a rotating photobioreactor. The method further includes optionally integrating the rotating photobioreactor with a composting or biogenic drying process.

Abstract: The present invention relates to polypeptides having phytase activity. These polypeptides have an amino acid sequence which has at least 70% identity to either of three phytases derived from the bacterium Buttiauxella, and which comprises at least one of the following amino acids at the position indicated: 119N, 120L, and/or 121E. These phytases have an improved specific activity. Additional specific amino acid substitutions are also disclosed which characterize and distinguish additional phytases of the invention having improved properties such as temperature and/or pH stability, pH activity profile, temperature activity profile, substrate profile, improved performance in animal feed in vitro or in vivo. The invention also relates to isolated polynucleotides encoding the polypeptides, nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

Abstract: The present invention provides for a method of genetically modifying microorganisms to enhance resistance to ionic liquids, host cells genetically modified in accordance with the methods, and methods of using the host cells in a reaction comprising biomass that has been pretreated with ionic liquids.

Abstract: The present invention relates to a process for the production of ethanol and butanol from biomass, and in particular to a process for the production of ethanol and butanol using two separate fermentation step subjecting the biomass feedstock to anaerobic fermentation at a pH below 6.0 and at a temperature in the range 20 to 700° C. and so as to convert the biomass to a product predominantly comprising acetic acid and butyric acid with at least a 2:1 ratio by weight of acetic acid to butyric acid, c) treating the product of stream of step (b) to separate a solution comprising the acetic acid and butyric acid by: (i) separating a solution comprising the acetic acid and butyric acid from any residual solids and (ii) separating bacteria and/or pasteurizing or sterilizing the solution from the first fermentation step, and d) in a second fermentation step fermenting the solution comprising the acetic acid and butyric acid from the step (c) to form ethanol and butanol.

Abstract: Fructose, e.g., fructose derived from a cellulosic or lignocellulosic material, is use, e.g., fermented to produce a product, e.g., a solvent.

Abstract: The present invention describes a method for producing butanol by fermentation of carbohydrates using mixed populations of acidogenic-phase cells and solventogenic-phase cells of Clostridium in a solitary vessel. The present system as described does not require intermittent adjustment of pH or venting of headspace gases. The method provides a process for removal of the butanol product which does not irreversibly harm the cells and conditions are described where such cells may resume butanol synthesis in the same solitary vessel. The invention also describes compositions and biologically pure cultures which comprise the Clostridium cells as disclosed.

Abstract: Provided herein are recombinant yeast host cells and methods for their use for production of isobutanol. Yeast host cells provided comprise an isobutanol biosynthetic pathway and at least one of reduced or eliminated aldehyde dehydrogenase activity, reduced or eliminated acetolactate reductase activity; or a heterologous polynucleotide encoding a polypeptide having ketol-acid reductoisomerase activity.

Abstract: The present invention relates to a method of identifying a heterologous polypeptide having enzymatic activity for converting pyruvate, acetaldehyde or acetate into acetyl-CoA in (the cytosol of) a yeast cell comprising: a) providing a mutated yeast cell comprising a deletion of at least one gene of the (PDH) by-pass, selected from the genes encoding the enzymes pyruvate decarboxylase (PDC), acetaldehyde dehydrogenase (ALD), and acetyl-CoA synthetase (ACS); b) transforming said mutated yeast cell with an expression vector comprising a heterologous nucleotide sequence encoding a candidate polypeptide having potential enzymatic activity for converting pyruvate, acetaldehyde or acetate into acetyl-CoA; c) testing said recombinant mutated yeast cell for its ability to grow on minimal medium containing glucose as sole carbon source, and d) identifying said candidate polypeptide as a heterologous polypeptide having enzymatic activity for converting pyruvate, acetaldehyde or acetate into acetyl-CoA in (the cytosol of

Abstract: Provided herein are recombinant yeast host cells and methods for their use for production of isobutanol. Yeast host cells provided comprise an isobutanol biosynthetic pathway and at least one of reduced or eliminated aldehyde dehydrogenase activity, reduced or eliminated acetolactate reductase activity; or a heterologous polynucleotide encoding a polypeptide having ketol-acid reductoisomerase activity.

Abstract: The present invention relates to an apparatus and a method for fermenting, separating, and refining a product, which is produced by cultivating a microorganism. The apparatus and the method for fermenting, separating, and refining, of the present invention, can separate and refine the product that is produced by microbial fermentation in a simple, continuous manner and with high efficiency.

Abstract: A group of bacterial dihydroxy-acid dehydratases having a [2Fe-2S] cluster was discovered. Bacterial [2Fe-2S] DHADs were expressed as heterologous proteins in bacteria and yeast cells, providing DHAD activity for conversion of 2,3-dihydroxyisovalerate to ?-ketoisovalerate or 2,3-dihydroxymethylvalerate to ?-ketomethylvalerate. Isobutanol and other compounds may be synthesized in pathways that include bacterial [2Fe-2S] DHAD activity.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful products, such as fuels. For example, systems can use feedstock materials, such as cellulosic and/or lignocellulosic materials and/or starchy materials, to produce ethanol and/or butanol, e.g., by fermentation.

Abstract: Lactic acid bacterial (LAB) cells were modified such that they have a specific activity of dihydroxy-acid dehydratase enzyme activity that is increased to about 0.1 ?mol min?1 mg?1. LAB cells with even higher activities of 0.2 to 0.6 ?mol min?1 mg?1 of DHAD activity were obtained. These modified cells may be used to produce isobutanol when additional isobutanol biosynthetic pathway enzymes are expressed.

Abstract: Yeast cells with reduced activity of certain enzymes involved in branched chain amino acid biosynthesis in yeast mitochondria are described. Target enzymes include threonine deaminase, isopropylmalate synthase, and optionally branched chain amino acid transaminase.

Abstract: The present invention relates to processes and systems for the production of fermentative alcohols such as ethanol and butanol. The present invention also provides methods for separating feed stream components for improved biomass processing and productivity.

Abstract: The subject invention pertains to the discovery that the NADH-dependent propanediol oxidoreductase (FucO) can reduce furfural. This allows for a new approach to improve furfural tolerance in bacterial and/or yeast cells used to produce desired products. Thus, novel biocatalysts (bacterial, fungal or yeast cells) exhibiting increased tolerance to furfural and 5-hydroxymethylfurfural (5-HMF) are provided as are methods of making and using such biocatalysts for the production of a desired product.

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: The present invention relates to recombinant microorganisms comprising biosynthetic pathways and methods of using said recombinant microorganisms to produce various beneficial metabolites. In various aspects of the invention, the recombinant microorganisms may further comprise one or more modifications resulting in the reduction or elimination of 3 keto-acid (e.g., acetolactate and 2-aceto-2-hydroxybutyrate) and/or aldehyde-derived by-products. In various embodiments described herein, the recombinant microorganisms may be microorganisms of the Saccharomyces clade, Crabtree-negative yeast microorganisms, Crabtree-positive yeast microorganisms, post-WGD (whole genome duplication) yeast microorganisms, pre-WGD (whole genome duplication) yeast microorganisms, and non-fermenting yeast microorganisms.

Abstract: A fermentation liquid feed including water and a product alcohol and optionally CO2 is at least partially vaporized such that a vapor stream is produced. The vapor stream is contacted with an absorption liquid under suitable conditions wherein an amount of the product alcohol is absorbed. The portion of the vapor stream that is absorbed can include an amount of each of the water, the product alcohol and optionally the CO2. The temperature at the onset of the absorption of the vapor stream into the absorption liquid can be greater than the temperature at the onset of condensation of the vapor stream in the absence of the absorption liquid. The product alcohol can be separated from the absorption liquid whereby the absorption liquid is regenerated. The absorption liquid can include a water soluble organic molecule such as an amine.

Abstract: A system and method for harvesting and processing algae, the system and method including harvesting algae by mechanical or chemical system and processing the harvested algae to produce at least one of biodiesel, biosolvents, bioplastics, biogas, or fertilizer.

Abstract: An improved process for alcohol production includes microbial fermentation using a genetically modified microorganism to produce substantial quantities of aldehydes that are stripped from the fermentation medium and condensed. So produced aldehydes are converted in an ex vivo process to corresponding alcohols.

Abstract: The present invention relates to producing chemicals and biofuels from wood material, e.g. mixed forest biomass. Specifically, the invention concerns a process for conditioning spent liquor produced by SO2-ethanol-water (SEW) fractionation of wood chips for fermentation to butanol, ethanol and acetone/isopropanol (so called ABE process) by Clostridia bacteria.

Abstract: A system and method for the treatment of biomass comprising mixing a biomass with an ionic liquid (IL) to swell the biomass and electromagnetic (EM) heating, preferably radiofrequency (RF) heating, said biomass. Additionally, a method of acidolysis of biomass comprising mixing biomass in an ionic liquid (IL) to swell the biomass; adding an acid, to lower the pH of the biomass below pH 7; applying radio frequency (RF) heating to the biomass to heat to a target temperature range; applying ultrasonic heating, electromagnetic (EM) heating, convective heating, conductive heating, or combinations thereof, to the biomass to maintain the biomass at a target temperature range; washing the treated biomass; and recovering sugars and released lignin.

Abstract: Provided herein are methods of increasing the efficiency of biomass saccharification. In particular, the methods include ways of avoiding feedback inhibition during the production of useful products.

Abstract: Methods and systems for producing a biofuel using genetically modified iron-oxidizing bacteria (IOB) are disclosed. In some embodiments, the methods include the following: providing an IOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel or chemical; feeding a first source of ferrous iron to the IOB; feeding water, carbon dioxide, and oxygen to the IOB; and producing at least the biofuel or chemical, ferric iron, and an IOB biomass. In some embodiments, the methods and systems include the following: a bioreactor including IOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel; a first source of ferrous iron; sources of water, carbon dioxide, and oxygen; and a electrochemical reactor that is configured to electrochemically reduce ferric iron produced in the bioreactor to a second source of ferrous iron.

Abstract: The invention relates to suitable screening strategies for evaluating various candidate promoters for differential gene expression during the propagation and production phases of a fermentation process. The invention also relates to recombinant host cells that comprise identified promoter nucleic acid sequences and methods for producing fermentation products employing the same.

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: Designer Calvin-cycle-channeled and hydrogenotrophic biofuel-production pathways, the associated designer genes and designer transgenic organisms for autotrophic production of butanol and related higher alcohols from carbon dioxide, hydrogen, and/or water are provided. The butanol and related higher alcohols include 1-butanol, 2-methyl-1-butanol, isobutanol, 3-methyl-1-butanol, 1-hexanol, 1-octanol, 1-pentanol, 1-heptanol, 3-methyl-1-pentanol, 4-methyl-1-hexanol, 5-methyl-1-heptanol, 4-methyl-1-pentanol, 5-methyl-1-hexanol, and 6-methyl-1-heptanol. The designer autotrophic organisms such as designer transgenic oxyphotobacteria and algae comprise designer Calvin-cycle-channeled and hydrogenotrophic pathway gene(s) and biosafety-guarding technology for enhanced autotrophic production of butanol and related higher alcohols from carbon dioxide and water.

Abstract: Methods for the evolution of NADPH specific ketol-add reductoisomerase enzymes to acquire NADH specificity are provided. Specific mutant ketol-acid reductoisomerase enzymes isolated from Pseudomonas that have undergone co-factor switching to utilize NADH are described.

Abstract: Increasing tolerance to butanol in yeast has been accomplished by decreasing activity of Pdr5p encoded by an endogenous PDR5 gene. A deletion mutation of the PDR5 gene led to improved growth yield in the presence of butanol. Yeast cells with reduced Pdr5p activity, or other multidrug resistance ATP-binding cassette transporter protein activity encoded by CDR1 or BFR1, and a butanol biosynthetic pathway may be used for improved butanol 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 allows 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 microorganism-containing biocatalysts disclosed have a large population of the microorganisms irreversibly retained in the interior of the biocatalysts. The biocatalysts possess a surprisingly stable population of microorganisms and have an essential absence of debris generation from metabolic activity of the microorganisms. The biocatalysts are composed of highly hydrophilic polymer and have an internal, open, porous structure that promotes community phenotypic changes.

Abstract: Overlay processes are disclosed for making ethanol that not only increase ethanol conversion but do so in a cost effective manner with a reduction in energy requirements per unit of ethanol production. The processes can provide, if desired, higher organic compound as a co-product with ethanol.

Abstract: A process that generates sulfide in production of liquid products from syngas and a system for syngas fermentation including a sulfide generation process to convert feed gas to liquid product, the process including: partially oxidizing high-temperature gas, input gas, and molten sulfur to generate sulfide gas, the high-temperature gas containing oxygen, the input gas containing carbonaceous fuel and the sulfide gas containing hydrogen sulfide, CO, CO2, and H2; mixing the sulfide gas with the feed gas to generate mixed gas having a predetermined hydrogen sulfide concentration; providing at least a portion of the mixed gas to a production fermentor containing microorganisms; and converting the mixed gas to the liquid product by contact with the microorganisms.

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: This invention relates to compositions, systems, and methods for producing biofuels, such as butanol, and related compounds. More specifically, provided are methods of making recombinant microorganisms having non-naturally occurring metabolic pathways for the production of biofuels, and methods of producing biofuels using such organisms. Also provided are metabolically engineered microorganisms capable of producing butanol from a substrate.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed for use in the production of useful products, such as fuels. For example, systems can use biomass materials, such as cellulosic and/or lignocellulosic materials, to enhance the production of a product, e.g., the production of ethanol and/or butanol by fermentation.

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 high flux of metabolites from pyruvate to 2,3-butanediol in Lactobacillus plantarum was achieved through genetic engineering. Substantial elimination of lactate dehydrogenase activity in the presence of heterologously expressed butanediol dehydrogenase activity led to 2,3 butanediol production that was at least 49% of the total of major pyruvate-derived products.

Abstract: The invention provides an improved method for the production, separation and recovery of one or more fermentation products from a fermentation broth. Further, the invention provides a method for increasing efficiency of a fermentation reaction.

Abstract: The invention relates to a process of producing a fermentation product in the presence of pyridoxamine.

Abstract: One or more genes in a biosynthesis pathway for a vitamin or other essential nutrient which is needed for the survival of a microorganism can be used as an effective selective marker to identify cells transformed with an exogenous nucleic acid. The microorganism does not naturally contain or express the one or more gene. This permits genetic manipulations to be performed. It permits lower cost fermentations to be performed. It permits production of the essential nutrient for subsequent commodity use.

Abstract: The invention relates to recombinant microorganisms that have been engineered to produce various chemicals using genes that have been repurposed to create a reverse beta oxidation pathway. Generally speaking, the beta oxidation cycle is expressed and driven in reverse by modifying various regulation points for as many cycles as needed, and then the CoA thioester intermediates are converted to useful products by the action of termination enzymes.