WO2020252335A1 - Processes and systems for producing products by fermentation - Google Patents

Abstract

Processes and systems for producing one or more products by fermentation, wherein a feed gaseous mixture is generated, fed into a bioreactor comprising hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product, wherein a gas stream from the bioreactor is conditioned and recycled back into the process and a liquid stream from the bioreactor is processed for purification of the at least one fermentation product.

Description

PROCESSES AND SYSTEMS FOR PRODUCING PRODUCTS BY FERMENTATION

CROSS REFERENCE TO RELATED APPLICATIONS

[0001 ] This application claims priority to U.S. Provisional Application No. 62/861 ,707, filed June 14, 2019, the disclosures of which are incorporated herein by reference.

FIELD

[0002] Disclosed herein are processes and systems for producing biological products by fermentation.

BACKGROUND

[0003] Numerous chemical processes have been developed for the production of amino acids, alcohols, carboxylic acids, ketones, hydroxy acids, and other useful chemicals. Many of these processes, however, utilize toxic reagents and/or solvents. Production processes that generate less toxic waste and/or are more energy efficient are desirable. Biological production systems are being used to produce biofuels and other commodity chemicals. The power of using biological processes for chemical production is twofold: first, renewable carbon sources can serve as substrates, and second, the range and specificity of molecules that can be made biologically surpasses that of synthetic chemistry. Biological production systems can utilize a variety of feedstock but gaseous feedstock could potentially be lower cost than other feedstocks. Anaerobic microbes have been demonstrated to produce ethanol from CO, CO2, and H2 via the acetyl CoA biochemical pathway. Thus, there is a need for efficient, highly yielding processes that utilize microbes to convert gas substrates into commodity chemicals.

SUMMARY

[0004] In one aspect, disclosed herein are processes for producing one or more product by fermentation. The processes comprise a) feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2; (b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic

microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (c) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2; (d) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and at least one fermentation product; and (e) separating the hydrogenotrophic

microorganisms from the liquid stream and recycling the hydrogenotrophic

microorganisms back to the bioreactor.

[0005] Another aspect of the present disclosure provides processes for producing one or more product by fermentation. The processes comprise (a) feeding an organic substrate into one or more reactor under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2; (b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains

hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (c) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2; and (d) recycling at least a portion of the gas stream back to the one or more reactors or the bioreactor.

[0006] A further aspect of the present disclosure encompasses processes for producing one or more product by fermentation. The processes comprise (a) feeding an organic substrate into one or more reactor under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2; (b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (c) removing a liquid stream from the bioreactor; (d) separating

hydrogenotrophic microorganisms from the liquid stream; and (e) recycling the hydrogenotrophic microorganisms to the bioreactor.

[0007] Still another aspect of the present disclosure provides processes for purifying one or more fermentation products from a fermentation liquid stream. The processes comprise (a) culturing hydrogenotrophic microorganisms in a bioreactor under fermentative conditions to produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (b) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and one or more fermentation product; and (c) purifying the one or more fermentation product from the liquid stream.

[0008] Yet another aspect of the present disclosure encompasses processes for producing one or more products by fermentation. The processes comprise (a) feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2; (b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the

hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (c) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and at least one fermentation product; (d) purifying the at least one fermentation product from the liquid stream, wherein the purification requires at least one procedure where water is removed from the liquid stream; and (e) recycling the water back to the one or more reactors of step (a), and/or to the bioreactor of step (b), and/or to a clean water hold tank.

[0009] A further aspect of the present disclosure provides systems for preparing one or more product by fermentation. The systems comprise (a) one or more reactors that converts an organic substrate into a gaseous mixture comprising COx and H2, where x is 1 and/or 2; (b) a bioreactor containing non-natural hydrogenotrophic microorganisms that convert the gaseous mixture to at least one fermentation product at a higher level than a parent hydrogenotrophic microorganism, wherein at least one fermentation product is chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; and (c) at least one separation device that remove at least some of H2S, CO2, or H2 from a gas stream exiting the bioreactor.

[00010] Other features and aspects of the processes are described in more detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

[0010] Figure 1 diagrams an embodiment of the overall process showing recycle streams.

[0011 ] Figure 2 illustrates an alternate arrangement of components that may be used to effect process 100, wherein multiple bioreactors are used in parallel.

[0012] Figure 3 illustrates recycle of the gas stream to the reactor regenerating H2 and COx.

[0013] Figure 4 diagrams separation of the liquid stream into a retentate that is recycled back to the bioreactor and filtrate comprising the fermentation products.

[0014] Figure 5 illustrates recycle of the gas stream and recycle of the retentate.

[0015] Figure 6 diagrams an embodiment in which organic substrate (methane) is fed into two reactors, a steam methane reformer followed by a water gas shift unit.

[0016] Figure 7 illustrated removal of H2 from the gas stream prior to recycle back to the steam methane reformer.

[0017] Figure 8 diagrams H2S removal and H2 removal from the gas stream prior to recycle back to the steam methane reformer.

[0018] Figure 9 illustrates an embodiment in which the gaseous mixture from the reactors (i.e. , steam methane reformer and water gas shift unit) enters a H2 separator 125 to remove some of the H2 in the gaseous mixture before it enters the bioreactor 115. [0019] Figure 10 diagrams an embodiment showing purification of the one or more fermentation products, with recycle of retentate and/or depleted retentate back to the bioreactor 115 and recycle of water removed during the purification process to a clean water tank.

DETAILED DESCRIPTION

[0020] The present disclosure encompasses microbial fermentation processes for producing commodity chemicals of interest. The processes comprise feeding a carbon source into one or more reactors that generate a feed gas mixture that is fed directly into a pressurized gas fermentation bioreactor, which improves mass transfer, increasing product yield, and reduces consumption of energy and utilities. Further, the subsequent gaseous products from the fermenter are treated and recycled back to the one or more reactors. Recycle of the hydrocarbon feed gas, purified via methods such as non-activated amines, improves gas utilization and lowers raw material cost. Flydrogen purification, for example via membrane separation or pressure swing absorption, further leads to purified hydrogen that is then used efficiently as feed for hydrogen sulfide synthesis. Hydrogen sulfide separation, recovery, and reuse also improves process efficiency. In addition, partial crystallization of the product in combination with recycling of the mother liquor back to the fermenter leads to enhanced product yield and minimized waste generation.

(I) Processes for Producing Products by Fermentation

[0021 ] In one embodiment, processes disclosed herein comprise (a) feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising H2 and CO, CO2, or CO and CO2; (b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product; (c) removing a gas stream from the bioreactor and optionally recycling at least a portion of the gas stream back to one of more reactors or the bioreactor; (d) removing a liquid stream from the bioreactor comprising fermentation broth containing the one or more fermentation products and the hydrogenotrophic microorganisms, separating the hydrogenotrophic microorganisms from the liquid stream, and optionally recycling the hydrogenotrophic microorganisms back to the bioreactor, and (e) purifying the one or more fermentation products from the liquid stream. The purification may comprise at least one procedure in which water is removed from the liquid steam, such that the water may be recycled back to one or more reactors, the bioreactor, a clean water hold tank, or other places in the process.

[0022] In another embodiment, processes disclosed herein comprise (a) feeding a gaseous mixture comprising H2 and CO, CO2, or CO and CO2, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product; (b) removing a gas stream from the bioreactor and optionally recycling at least a portion of the gas stream back to one of more reactors or the bioreactor; (c) removing a liquid stream from the bioreactor comprising fermentation broth containing the one or more fermentation products and the hydrogenotrophic microorganisms, separating the hydrogenotrophic microorganisms from the liquid stream, and optionally recycling the hydrogenotrophic microorganisms back to the bioreactor, and (d) purifying the one or more fermentation products from the liquid stream. The purification may comprise at least one procedure in which water is removed from the liquid steam, such that the water may be recycled back to one or more reactors, the bioreactor, a clean water hold tank, or other places in the process.

(a) Feeding an organic substrate into one or more reactors to generate a gaseous mixture

[0023] In some embodiments, a process of the present disclosure comprises feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising H2, and CO, CO2, or CO and CO2. The combination of hydrogen gas with carbon monoxide and some carbon dioxide is commonly referred to as a“syngas.” Organic substrate

[0024] A variety of organic substrates are suitable for the generation of the gaseous mixture, and each organic substrate may be used alone or in combination with other organic substrates. Non limiting examples of suitable organic substrates include biomass, biogas, off-gas, natural gas, natural gas liquid, oil, and carbonaceous material.

[0025] In some embodiments, the organic substrate may be biomass. As used herein,“biomass” refers to any animal or plant material used as a raw material, whether purposefully grown or cultivated, or whether a waste material from plants or animals that is not used for food or feed. Biomass may be purposefully grown woody, herbaceous or aquatic plants (e.g., algae, clover, grasses ( Miscanthus species,

Sudangrass, switchgrass, etc.), maize, millet, poplar, seaweed, sorghum, willow, etc.), wood or forest residue (e.g., bark, scrap lumber, mill residuals, wood left behind as part of logging, forest debris, peat, clearance wood or prunings from orchards, etc.), waste from farming (e.g., stover, straw, etc.), waste from horticulture (e.g., yard waste, tree trimmings), waste from food processing (e.g., bagasse, cobs, hulls, pulp, oil palm empty fruit bunch, palm kernel cake, palm oil mill effluent, animal parts, etc.), waste from animal farming (e.g., manure, urine, etc.), human waste (e.g., from sewage plants), food waste from groceries or restaurants, or by-products of industrial processes (e.g., lignin or other material from the paper pulping industry, etc.) and the like. In various

embodiments, the biomass may be cellulose-containing feedstocks, animal tissue, fish tissue, plant parts, fruits, vegetables, plant-processing waste, animal-processing waste, animal manure, animal urine, mammalian manure, mammalian urine, solids isolated from fermentation cultures, bovine manure or urine, poultry manure or urine, equine manure or urine, porcine manure or urine, wood shavings, wood chips, wood pulp, sawdust, slops, pomace, shredded paper, cotton burrs, bagasse, grain, chaff, seed shells, hay, alfalfa, grass, leaves, sea shells, seed pods, stover, straw, corn cobs, corn shucks, weeds, aquatic plants, peat, seaweed, algae, fungus, or combinations thereof.

[0026] In other embodiments, the organic substrate may be biogas. As used herein, the term“biogas” refers to a mixture of gases produced by the breakdown of organic matter by microbial fermentation. Biogas may be produced from biomass, including but not limited to agricultural waste, manure, municipal waste, plant material, sewage, green waste or food waste.

[0027] In other embodiments, the organic substrate may be off-gas. As used herein, the term“off-gas” refers to a gas that is produced as a by-product of an industrial process or that is given off by a manufactured object or material. An off-gas may be produced by industrial plants including but not limited to petroleum refineries, chemical plants, and natural gas processing plants.

[0028] In still other embodiments, the organic substrate may be natural gas liquid (also called hydrocarbon gas liquid) or oil. Hydrocarbon gas liquids (HGL) are hydrocarbons that occur as gases at atmospheric pressure and as liquids under higher pressures. HGL can also be liquefied by cooling. The term“oil” includes crude oil, as well as fractions derived from the basic yield, including distillation and cracking fractions (e.g., bitumen, naphtha, etc.).

[0029] In additional embodiments, the organic substrate may be

carbonaceous material. As used herein, the term“carbonaceous material” refers to any solid material (mixture or compound) other than an inorganic carbonate which contains carbon or carbon containing compounds. Nonlimiting examples of carbonaceous material include coal, petcoke, resid, wood, and the like.

[0030] In other embodiments, the organic substrate may be a feedstock generated during ammonia synthesis, during methanol synthesis, or during steelmaking.

[0031 ] In specific embodiments, the organic substrate may be natural gas. In specific embodiments, the organic substrate may be wood or wood that has been mechanically processed (e.g., wood shavings, wood chips, wood pulp, sawdust, etc.). In specific embodiments, the organic substrate may be coal, petcoke, or resid. In specific embodiments, the organic substrate may be lignite coal, bituminous coal, or anthracite coal. In specific embodiments, the organic substrate may be a crude oil fraction obtained by distillation or cracking. In specific embodiments, the organic substrate may be a woody, herbaceous or aquatic plant grown solely for energy.

[0032] The organic substrate may be used as is, or may be further processed prior to its use in the process. For instance, animal or plant material may be further processed by grinding, milling, shaving, pelletizing, etc. Gaseous substrates may be conditioned by the selective removal or addition of components. As one example, when natural gas is the methane source, it may be conditioned by removing or reducing contaminants deleterious to the process. As a non-limiting example, natural gas may be conditioned by removing or reducing the sulfur content. For instance, natural gas may be passed through a sulfur removal unit. The sulfur removal unit may comprise a metal oxide (e.g., zinc oxide), molecular sieves, or amines for reaction and removal of a sulfur compound (e.g., H2S) from the natural gas. Alternatively, or in addition, a natural gas feed may also contain CO2, HCN and/or COS that needs to be reduced or eliminated. Established technologies to remove these contaminants are known in the art.

Reactors

[0033] The organic substrate, or a processed form thereof, is fed into one or more reactors for generation of the gaseous mixture. Suitable reactors include gasifiers, water gas shift reactors, steam methane reformer reactors, or other reactors that produces hydrogen, CO, CO2, and CO and CO2. Generally, the reactor is of tubular design comprising a single stage or multistage design. Further, the reactor may comprise a fixed bed, moving bed, or fluidized bed for maximum interaction between the reactants and catalyst, when present. Alternatively, the reactor may be an entrained flow reactor. In one embodiment, the reactor may comprise a steam methane reformer and water shift gas unit.

[0034] The one or more reactors may optionally contain one or more catalysts, which facilitate at least one reaction occurring therein. Water gas shift reactors and steam methane reformer reactors typically contain one or more catalysts, while a catalyst may not be present in a gasifier. In general, the catalyst comprises at least one alkali earth metal, at least one transition metal, at least one p-block metal, or combinations thereof. Non-limiting examples of these metals include aluminum, antimony, barium, bismuth, calcium, cerium, chromium, cobalt, copper, gold, iridium, iron, lanthanum, nickel, magnesium, molybdenum, palladium, platinum, rhenium, rhodium, ruthenium, samarium, silicon, strontium, titanium, thorium, tungsten, vanadium, yttrium, zirconium, or combinations thereof. In specific embodiments, the catalyst may comprise nickel, iron-chromium, or copper. [0035] The catalyst may be in various forms. Non-limiting examples of the forms or configuration the catalyst(s) include packing, an unstructured packing, a foil, a sheet, a screen, a wool, a wire, a ball, a plate, a pipe, a rod, a pellet, a bar, or a powder. In one embodiment, the form of the catalyst is a pellet.

Reactor conditions

[0036] The organic substrate and process steam are fed into the one or more reactors. The organic substrate may be blended with other sources of hydrogen, carbon monoxide or carbon dioxide to produce or make a gaseous mixture of the desired composition. Other sources of hydrogen, carbon monoxide or carbon dioxide include pipeline hydrogen, pipeline carbon dioxide, carbon dioxide scrubber off-gas, flue gas, ethane cracker off-gas, reformer off-gas or chlorine synthesis off-gas.

Alternatively, or in addition, additional gases may be fed into the one or more reactors, either as separate stream(s) or as a mixture with the organic substrate and/or process steam. Non-limiting examples of additional gases include oxygen (O2) or air (i.e. , a mixture of oxygen and nitrogen). The ratio or organic substrate to steam can and will vary depending for example upon the identity of the organic substrate. In embodiments in which the organic substrate is methane, the molar ratio of methane to steam may range from about 1 :2 to about 1 :4, e.g., the molar ratio may be about 1 :2, about 1 :2.5, about 1 :3, about 1 :3.5, about 1 :4, etc.

[0037] The organic substrates entering the reactor are at least partially converted into a gaseous mixture comprising hydrogen, carbon monoxide, and/or carbon dioxide. Stated another way, the organic substrate is converted to syngas or water-gas shifted syngas.

[0038] Specifically, hydrogen production involves a series of reforming, conditioning and separation steps wherein several of those steps (e.g., steam

reforming, autothermal reforming, gasification, high temperature shift, low temperature shift, CO2 scrubbing, amine scrubbing, and pressure swing absorption) can provide a gas mixture that by itself or in combination with one or more other gas streams can provide the gaseous mixture that is a substrate for production of one or more

fermentation products. [0039] By way of background, hydrogen production may involve single step or multistep reforming, partial oxidation, or gasification to produce a gaseous mixture such as syngas, combined with a high temperature water gas shift (HTS) reaction, a low temperature water gas shift (LTS) reaction, or both. In some methods, carbon oxides are removed by using pressure swing adsorption (PSA) with molecular sieves, which separates a substantially pure hydrogen (hte) gas stream from a tail gas comprising some residual H2 gas along with various amounts of carbon dioxide (CO2), carbon monoxide (CO), and methane (CPU). In certain embodiments, carbon dioxide may be optionally scrubbed before subjecting the gas (e.g., syngas) to PSA.

Depending on the syngas production process used and whether carbon dioxide is scrubbed, a tail gas will include different ratios of H2, CO2, CO, and CPU. In some embodiments, the gaseous mixture for use in the methods of this disclosure is a blend comprising a mixture of PSA tail gas and PI2 gas.

[0040] For example, methane steam reforming combined with PITS and LTS will produce gases having mostly PI2 (about 75%) and CO2 (about 20%), with some CPU (about 5%) and very little or no CO. In another example, methane steam reforming combined with PITS will produce gases having mostly PI2 (about 75%) and CO (about 10%), with some CO2 (about 5%) and CPU (about 1 %). In still another example, methane steam reforming combined with PITS and PSA will produce a tail gas having mostly PI2 (about 30%) and CO2 (about 45%), with a fair amount of CO (about 10%) and CPU (about 15%). In this last embodiment, if a CO2 scrubbing step is included, then the tail gas will comprise mostly PI2 (about 50%), CPU (about 30%) and CO (about 20%), with little CO2 (about 1 %). In certain embodiments, the PSA tail gas is mixed with the pipeline PI2 produced from PSA to produce a gaseous mixture comprising PI2 and COx, where x is 1 and/or 2 in which the ratio of CO2 to PI2 may range from 1 : 1 to about 1 :5.

[0041 ] Steam reforming of methane can provide a gaseous mixture having a molar ratio of CO2 to PI2 that ranges from about 1 :7 to about 1 :15, wherein other components may include CO, CPU and PI2O. Alternatively, methane may be reformed with CO2, which is called dry reforming. Dry reforming of methane can provide a gaseous mixture having a molar ratio of CO2 to PI2 that ranges from about 1 :5 to about 1 :15, respectively, wherein other components may include CO, CPU, and PI2O. [0042] Partial oxidation (catalytic or non-catalytic) and autothermal reforming of methane uses oxygen as a co-reactant, instead of water. Partial oxidation and autothermal reforming can provide a gaseous mixture having a molar ratio of CO2 to H2 that is about 1 :20, wherein other components may include CO, CPU, and H2O.

[0043] Gasification, the partial oxidation of carbonaceous material with air or oxygen can provide a gaseous mixture having a molar ratio of CO2 to H2 that ranges from about 1 :1.1 to about 1 :11 , wherein other components may include CO, CPU, N2, and PI2O.

[0044] In one embodiment, at least one of the following reactions occurs in the reactor:

CPU + PI2O -> CO + 3 PI2

In another embodiment, both reactions occur in the reactor. The first of the above two reactions is generally referred to as a methane reformer reaction, while the second is generally referred to as the water-gas shift reaction (WGSR).

[0045] The methane reforming reaction is also referred to as the steam reforming or steam methane reforming process, and is a catalytic reaction that converts steam and light hydrocarbons (e.g., methane) into hydrogen and carbon monoxide. The methane reforming reaction may be catalyzed by a nickel containing catalyst.

[0046] The temperature of the methane reforming reaction can and will vary depending on the organic substrate used the process, the scale of the process, and the catalyst utilized in the process. Generally, the temperature of the process may range from about 500 °C to about 1500 °C. In various embodiments, the temperature of the process may range from about 500 °C to about 1500 °C, from about 600 °C to about 1200 °C, from about 700 °C to about 1000 °C, or from about 850 °C to about 950 °C.

[0047] The pressure of the methane reforming reaction can and will vary depending on the organic substrate used in the process, the scale of the process, and the catalyst used. In general, the pressure of the methane reforming reaction may range from about 40 psi to about 400 psi. In various embodiments, the pressure of the process may range from about 40 psi to about 400 psi, from about 75 psi to about 300 psi, from about 100 psi to about 200 psi, or from about 125 psi to about 175 psi. [0048] The water gas shift reaction comprises catalytically converting the carbon monoxide and water from the methane reforming reaction by the addition of water vapor into carbon dioxide and hydrogen gas. The water gas shift reaction may be catalyzed by a catalyst comprising nickel, iron-chromium (for high temperature shift), or copper (for low temperature shift). A combination of a high temperature shift using an iron oxide-chromium oxide catalyst followed by a low temperature shift using a copper- based catalyst may be used.

[0049] The temperature of the water gas shift reaction process can and will vary depending on the organic substrate used in the process, the scale of the process, and the catalyst utilized in the process. Generally, the temperature of the process may range from about 200 °C to about 600 °C. In various embodiments, the temperature of the process may range from about 200 °C to about 600 °C, from about 300 °C to about 500 °C, or from about 325 °C to about 425 °C. In one embodiment, the temperature of the process is maintained at 370 ± 25 °C.

[0050] The pressure of the water gas shift reaction process can and will vary depending on the scale of the process and the catalyst used. In general, the pressure of the water gas shift reaction may range from may range from about atmospheric pressure (~14.7 psi) to about 1200 psi. In various embodiments, the pressure of the process may range from about 14.7 psi to about 1200 psi, from about 100 psi to about 1000 psi, from about 250 psi to about 750 psi, or from about 400 psi to about 600 psi.

[0051 ] The molar ratio of CO2 to H2 in the gaseous mixture exiting the one or more reactors may range from about 1 :50 to about 10:1 , respectively. In some embodiments, the molar ratio of CO2 to H2 may range from about 1 :20 to about 5:1. In other embodiments, the molar ratio of CO2 to H2 may range from about 1 : 10 to about 2:1. In certain embodiments, the molar ratio of CO2 to H2 may be about 1 :1 , about 1 :2, about 1 :3, about 1 :4, or about 1 :5. In embodiments, the molar ratio of CO2 to H2 may range from about 1 :3 to about 1 :5, or from about 1 :3.5 to about 1 :4. The gaseous mixture produced in the one or more reactors may be mixed with any other hte/COx mixture, or with H2, CO2, CO or any combination thereof, to produce a gaseous mixture of the desired composition. [0052] In preferred embodiments, the gaseous mixture exiting the one or more reactors may have an amount of CO of no more than about 35 mol%. In certain embodiments, the amount of CO in the gaseous mixture may be no more than about 20 mol%, or no more than about 8 mol%. In other embodiments, the amount of CO in the gaseous mixture may range from about 0.25 mol% to about 20 mol%. For instance, the concentration of CO in the gaseous mixture may range from about 0.25 mol% to about 1 mol%, from about 1 mol% to about 3 mol%, from about 3 mol% to about 5 mol%, from about 5 mol% to about 10 mol%, or from about 10 mol% to about 20 mol%. In specific embodiments, the amount of CO in the gaseous mixture may range from about 0.5 mol% to about 4 mol%.

[0053] The gaseous mixture exiting the one or more reactors may be conditioned after leaving the reactor. Conditioning the gaseous mixture includes adjusting the moisture content, removing undesired components, and/or adding desired components. In one embodiment the gaseous mixture may be conditioned by passing the gaseous mixture through a H2 separator to reduce the amount to H2 in the gaseous mixture (see Figure 9). The H2 separator may be a pressure swing adsorption unit or a hydrogen membrane. Pressure swing adsorption units may comprise carbon pellets that absorb everything but H2. Flydrogen membranes may comprise metal alloy, composite metal, and/or inorganic microporous (e.g., ceramic) membranes. In one embodiment, the gaseous mixture may be passed through a palladium-based

membrane which adsorbs H2. The H2 removed from the gaseous mixture may be used for other processes (e.g., production of H2S) or it may be purged.

[0054] Generally, the gaseous mixture exiting the one or more reactors is cooled to a temperature that is near the operating temperature of the bioreactor (e.g., about 25 °C to about 85 °C) through the use of at least one heat exchanger. Fleat captured from the gaseous mixture is captured for use in other parts of the process. For example, heat may after be used in a steam generator, where steam is generated for use in the one or more reactors. Alternatively, or in addition, the steam generated may be converted to electricity, for example, with a turbine. (b) Feeding the gaseous mixture and other substrates to a bioreactor

[0055] In the various embodiments of the present disclosure, a gaseous mixture comprising H2 and CO, CO2, or CO and CO2, a nitrogen source, and optionally a sulfur source are fed to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product.

Bioreactor

[0056] A variety of different bioreactors may be used in the processes disclosed herein. Liquid phase bioreactors (e.g., stirred tank, packed bed, one liquid phase, two liquid phase, hollow fiber membrane) are well known in the art and may be used for growth of hydrogenotrophic microorganisms in the processes disclosed herein. Multiphase bioreactors (e.g., bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), fluidized bed bioreactor) may be used in the processes disclosed herein. Bubble columns are devices in which gas, in the form of bubbles, come in contact with liquid. Trickle bed bioreactors use co-current or countercurrent flow of gas and liquid to grow cultures. A fluidized bed bioreactor comprises passing a fluid (gas or liquid) through a granular solid material at high enough velocities to suspend the solid and cause it to behave as though it were a fluid. One purpose of multiphase bioreactors is to mix the liquid and gas phases, wherein the gas is consumed by hydrogenotrophic microorganisms to a greater or lesser extent depending on the intensity of mass transfer and chemical reaction.

[0057] Non-limiting examples of suitable bioreactors include continuous stirred tank bioreactors, bubble column bioreactors, loop bioreactors, airlift bioreactors, fluidized bed bioreactors, packed bed bioreactors, trickle flow bioreactors, mechanically agitated fermenters, non-mechanically agitated fermenters, non-agitated fermenters, tower fermenters, deep jet fermenters, batch fermenters, cyclone column fermenters, gas lift fermenters, wave bioreactors, sparged tank fermenters, membrane bioreactors, novel see saw fermenters, rotary drum bioreactors, mist bioreactors, and photo bioreactors. In certain embodiments, the bioreactor may be a stirred tank, packed bed, one liquid phase, two liquid phase, hollow fiber membrane, bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), air lift, loop, or fluidized bed bioreactor. In specific embodiments, the bioreactor may be a continuously stirred tank reactor.

[0058] Generally, the bioreactor contains at least one inlet, which allows the gaseous mixture from the reactor to enter, and at least two outlets. One outlet allows for the removal of a liquid stream, which contains the one or more fermentation products, and the other outlet allows for the removal of a gas stream.

[0059] In an embodiment, two, three, four, five or more bioreactors may be used in the process. In one embodiment, at least two bioreactors are connected. In another embodiment, at least three bioreactors or at least four bioreactors are connected. In an embodiment, if multiple bioreactors are used, the bioreactors are attached in series. In another embodiment, if multiple bioreactors are used, the bioreactors are attached in parallel. In an embodiment, the bioreactors are isolated from other bioreactors, in order to prevent one bioreactor from possibly contaminating any other bioreactors that may be in use.

[0060] In some embodiments, hydrogenotrophic microorganisms and suitable fermentation medium may be added directly to a sterilized bioreactor.

Generally speaking, media compositions useful for culturing hydrogenotrophic microorganisms are known in the art. In other embodiments, hydrogenotrophic microorganisms and fermentation medium may be added to at least one starter bioreactor, where the microorganisms are allowed to grow to the desired density. This initial culture can be periodically or continuously added to a bioreactor to maintain the directed density of microorganisms in the bioreactor. Typically, the initial batch of microorganisms is grown in a starter bioreactor that is smaller than the bioreactors used in the disclosed processes. In an embodiment, at least some of the hydrogenotrophic microorganisms are cultured/grown in one or more starter bioreactors, before the hydrogenotrophic microorganisms are added to the bioreactor. In such embodiments, each of the one or more bioreactors is in liquid communication with a starter bioreactor (Figures 1 and 2). Microorganisms

[0061 ] The microorganisms used in the processes include natural and non-natural hydrogenotrophic microorganisms. The hydrogenotrophic microorganisms may be methanogenic archaea, Clostridium, or Knall-gas bacteria.

[0062] Examples of suitable methanogenic archaea include

microorganisms of a genus selected from Methanobacterium, Methanobrevibacter, Methanocalculus, Methanocaldococcus, Methanocella, Methanococcus,

Methanococcoides, Methanocorpusculum, Methanoculleus, Methanofollis,

Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,

Methanolobus, Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter,

Methanothermococcus, Methanothermus, Methanotorris, and mixtures of two or more thereof.

[0063] Exemplary methanogenic archaea species may include

Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae,

Methanobacterium formicicum, Methanobacterium ivanovii, Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum,

Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus,

Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocaldococcus vilosus, Methanocella arvoryzae, Methanocella conradii, Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii,

Methanothermococcus okinawensis, Methanothermus sociabilis, Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus,

Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanotorris formicicus, Methanotorris igneus, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta

thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila, Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus thermolithotrophicus, Methanopyrus kandleri,

Methanothermobacter thermoautotroiphicus, Methanocaldococcus fervens,

Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, Methanocaldococcus vulcanius, and mixtures of two or more thereof.

[0064] Methanogenic archaea produce cytochromes or do not produce cytochromes. In some embodiments, the hydrogenotrophic microorganism may be a methanogenic archaea that does not produce cytochromes. Examples include

Methanococcus maripaludis or Methanococcus vannielii. In other embodiments, the hydrogenotrophic microorganism may be a methanogenic archaea that does produce cytochromes, which includes Methanosarcina barkeri or Methanosarcina mazei.

[0065] In related embodiments, a methanogenic archaea used herein may be mesophilic, thermophilic or hyperthermophilic. Exemplary mesophilic methanogens include some species of Methanobacterium, Methanobrevibacter, Methanocalculus, Methanocaldococcus, Methanococcus, Methanocorpusculum, and Methanosarcina. Exemplary thermophilic methanogens include some species of Methanomicrobium, Methanosaeta, Methanosarcina, and Methanothermococcus. Exemplary

hyperthermophilic methanogens include some species of Methanocaldococcus,

Methanopyrus, Methanothermus, and Methanotorris.

[0066] In further embodiments, the hydrogenotrophic microorganisms may be bacteria. In certain embodiments, the hydrogenotroph may be a syngas or CO metabolizing microorganism, such as Clostridium, Moorella, Pyrococcus, Eubacterium, Acetogenium, Acetobacterium, Desulfobacterium, Acetoanaerobium, Butyribaceterium, Carboxydothermus, or Peptostreptococcus. Exemplary Clostridium species include C. autoethanogenum, C. Ijungdahli, C. ragsdalei, C. carboxydivorans, C. woodii, and C. neopropanologen and an exemplary Butyribaceterium species is B. methylotrophicum.

In certain other embodiments, the hydrogenotroph may be Knall-gas bacteria, such as Cupriavidus necator, Hydrogenobacter thermophilus, Hydrogenovibrio marinus, or Helicobacter pylori.

[0067] In certain embodiments, the hydrogenotrophic microorganism may be an obligate hydrogenotroph or a facultative hydrogenotroph. In further

embodiments, the hydrogenotrophic microorganism may be an obligate anaerobe or a facultative anaerobe. In certain embodiments, a hydrogenotrophic facultative anaerobe may grow in the presence of H2 and oxygen or oxide (e.g., iron oxides, amine oxides, phosphine oxides, sulfoxides). Exemplary hydrogenotrophic facultative anaerobes include Cupriavidus (e.g., C. alkaliphilus, C. basilensis, C. campinensis, C. gilardii, C. laharis, C. metallidurans, C. necator, C. numazuensis, C. oxalaticus, C. pampae, C. pauculus, C. pinatubonensis, C. respiraculi, C. taiwanensis), Hydrogenobacter thermophilus, Xanthobacter autotrophicus, Rhodococcus opacus, Rhodopseudomnas sp., and Alicaligenes sp.

[0068] The hydrogenotrophic microorganisms may be engineered (e.g., non-natural), to knock-out, reduce, express or over-express polypeptides of interest, which results in engineered microorganisms useful for converting (e.g., utilizing, converting, assimilating, oxidizing, reducing) various components of gaseous mixture of substrate into one or more useful fermentation products (e.g., amino acids).

[0069] Genetic manipulation to engineer hydrogenotrophic

microorganisms may include site-directed mutagenesis (e.g., of one or more gene targets), alteration of regulatory sequences or sites associated with expression of one or more gene targets (e.g., by removing strong, weak, inducible, repressible, or multiple promoters, or by replacing such promoters with promoters having different properties), changing the chromosomal location of one or more gene targets, altering nucleic acid sequences adjacent to one or more gene targets (such as a ribosome binding site or transcription terminator), decreasing or increasing the copy number of one or more gene targets, modifying regulatory proteins, repressors, suppressors, enhancers, transcriptional activators or the like involved in transcription of one or more gene targets or translation of one or more gene products, or any other method of deregulating expression of one or more gene targets (including the use of antisense nucleic acid molecules, short interfering nucleic acid molecules, or other methods to knock-out or block expression of a target protein).

[0070] Variation in codon usage bias has been observed across different species of bacteria and archaea, which may affect recombinant protein expression in a heterologous host (Sharp et al. , Nucl. Acids Res. 33:1141 , 2005; Emery and Sharp,

Biol. Lett. 7:131 , 2011 ). In certain embodiments, nucleic acid molecules may be codon optimized prior to introduction into hydrogenotrophic microorganisms to improve or maximize protein expression. Codon optimization refers to the alteration of codon sequence in genes or coding regions at the nucleic acid molecule level to reflect a more common codon usage of a host cell without altering the amino acid encoded by the codon. Codon optimization methods for gene expression in heterologous hosts have been previously described (see, e.g., Welch et al., Methods Enzymol. 498:43, 2011 ; Henry and Sharp, Mol. Biol. Evol. 24:10, 2007; U.S. Patent Publication No.

2011/0111413).

[0071 ] In further embodiments, endogenous or exogenous nucleic acid molecules encoding a biosynthetic enzyme may be altered, such as having the amino acid sequence changed from wild-type. Each variant polypeptide generated by these methods will retain at least 50% activity (preferably 100% or more activity) and have a polypeptide sequence that is at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical, or 100% identical to a reference or parental wild-type polypeptide sequence. In certain embodiments, variant polypeptides will include at least one amino acid substitution (e.g., at least 1 , 2, 3, 5, 6, 7, 8, 9 or 10 or more or up to 20, 25, or 30 substitutions) or no more than a particular number of amino acid substitutions (e.g., no more than 1 , 2, 3, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 substitutions) at one or more pre-determ ined positions relative to a reference or parental wild-type enzyme, provided that a variant retains an activity of interest (e.g., aspartokinase, carboxylase, decarboxylase, dehydrogenase, epimerase, kinase, lyase, reductase, synthase).

[0072] Any of the hydrogenotrophic microorganisms of this disclosure may be transformed to comprise at least one exogenous nucleic acid to provide the host with a new or enhanced activity (e.g., enzymatic activity) or may be genetically modified to remove, substantially reduce, or overexpress an endogenous gene function using any of a variety of methods known in the art. Genetic tools for transfer and expression of heterologous nucleic acid molecules in hydrogenotrophic microorganisms, such as methanogenic archaea, are known in the art (see, e.g., Rother et al. , Curr. Opin.

Microbiol. 8:745, 2005; Leigh et al., FEMS Microbiol. Rev. 35:577, 2011 ). For example, tools are available for DNA delivery (Dodsworth et al., Appl. Environ. Microb. 76:5644, 2010; Metcalf et al., Proc. Natl. Acad. Sci. U. S. A. 94:2626, 1997), for shuttle vectors (Gardner and Whitman, Genetics 152:1439, 1999; Metcalf et al., 1997), for regulated expression of heterologous genes (Lie and Leigh, J. Bacteriol. 184:5301 , 2002; Chaban et al., Mol. Microbiol. 66:596, 2007; Guss et al., Archaea 2:193, 2008), and for knock-in or knock-out genetic exchange (Moore and Leigh, J. Bacteriol. 187:972, 2005; Pritchett et al., App. Environ. Microb. 70:1425, 2004). Therefore, various methods for

inactivating, knocking-out, or deleting endogenous gene function in hydrogenotrophic microorganisms may be used.

[0073] In certain embodiments, a hydrogenotrophic microorganism may be a microorganism disclosed in WO2015103497 or WO2016179545, each of which is hereby incorporated by reference in its entirety.

[0074] In some embodiments, promoters, codon optimization, or both can be used for high, constitutive expression of exogenous nucleic acid molecules encoding biosynthesis pathway enzymes in host hydrogenotrophic microorganisms. Regulated expression of an exogenous nucleic acid molecule in a host hydrogenotrophic microorganism (e.g., methanogenic archaea) may also be utilized. In certain

embodiments, regulated expression of exogenous nucleic acid molecules encoding biosynthesis enzymes may be desirable to optimize growth rate of the non-natural or recombinant hydrogenotrophic microorganisms. Controlled expression of nucleic acid molecules encoding biosynthesis enzymes for response to the presence of the gaseous mixture of substrates may improve growth based on the variety of different sources or ratios of substrate available.

[0075] In certain embodiments, the hydrogenotrophic microorganism may be genetically modified or engineered to produce at least one fermentation product at a higher level that a parental hydrogenotrophic microorganism. The engineered hydrogenotrophic microorganism may produce at least one fermentation product at a level that is at least about 10% greater than that produced by the parent

hydrogenotrophic microorganism, or at least about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 6-fold, about 7-fold, about 8-fold, about 9-fold, about 10-fold, about 15-fold, about 20-fold, about 30-fold, about 40-fold, about 50-fold, about 60-fold, about 70-fold, about 80-fold, about 90-fold, about 100-fold, about 500-fold, or about 1000-fold, or about 10,000-foldthe level produced by the parent hydrogenotrophic microorganism, when cultured under the same culture conditions. In other embodiments, the

engineered hydrogenotrophic microorganism may produces at least one fermentation product at a level that is from at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or is at least about 95% greater than that produced by the parent hydrogenotrophic microorganism under the same culture conditions.

[0076] Hydrogenotrophic microorganisms described herein may be grown as an isolated pure culture, with a heterologous non-hydrogenotrophic microorganism(s) that may aid with growth, or combined with one or more different strains or species of hydrogenotrophic microorganisms to generate a mixed culture.

Substrates

[0077] The substrates entering the bioreactor may be collectively referred to as“the bioreactor feed.” The bioreactor feed comprises H2, CO and/or CO2, a nitrogen source, and optionally a sulfur source.

[0078] The bioreactor and the one or more reactors from Section (l)(a) may be in series, such that the gaseous mixture exiting the one or more reactors is fed to the bioreactor with or without further conditioning. Alternatively, or in addition, a gaseous mixture comprising H2 and CO, CO2, or CO and C02 may be provided from a different source. For instance, in some embodiments, a process of the present disclosure comprises feeding a gaseous mixture exiting the one or more reactors from Section (l)(a), a gaseous mixture from a recycle stream, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic

microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product.

[0079] A variety of different nitrogen sources may be used. Suitable nitrogen sources include ammonia (Nhh) and ammonia derivatives (e.g., ammonium hydroxide, ammonium acetate, etc.), as well as nitrogen gas (N2), nitric oxide (NO), nitrous oxide (N2O), or any combination thereof. The nitrogen source may be

purchased or it may be generated on site. In one embodiment, a nitrogen source may be NH3 or a derivative thereof.

[0080] Suitable sulfur sources include hydrogen sulfide (H2S) and sulfide derivatives (e.g., sodium sulfide, potassium sulfide, ammonium sulfide, methyl sulfide, dimethyl sulfide, carbonyl sulfide, etc.), as well as bisulfate, thiosulfate, sulfuric acid, sodium sulfate, sulfur oxides, or any combination thereof. The sulfur source may be purchased or it may be generated on site. In specific embodiments, the sulfur source may be H2S or a derivative thereof.

[0081 ] In specific embodiments, the bioreactor feed may comprise about 7 wt% to about 20 wt% of H2, about 0.5 wt% to about 12 wt% of CO, about 30 wt% to about 85 wt% of CO2, about 0.1 wt% to about 5 wt% of Nhh, and about 0.1 wt% to about 9 wt% of hhS. For instance, Nhh may be about 0.1 wt%, about 0.5 wt%, about 0.75 wt%, about 1.0 wt%, about 1.5 wt%, about 2 wt%, about 3 wt%, about 4 wt%, or about 5 wt% of the bioreactor feed. hhS may be about 0.1 wt%, about 0.5 wt%, about 0.75 wt%, about 1.0 wt%, about 2 wt%, about 3 wt%, about 4 wt%, or about 5 wt%, about 6 wt%, about 7 wt%, about 8 wt%, or about 9 wt% of the bioreactor feed.

[0082] In further embodiments, the bioreactor feed may comprise about 10 wt% to about 15 wt% of hh, about 1 wt% to about 10 wt% of CO, about 70 wt% to about 80 wt% of CO2, about 1 wt% to about 3 wt% of Nhh, and about 1 wt% to about 5 wt% of hhS.

[0083] In an exemplary embodiment, the bioreactor feed may comprise about 14 wt% of hh, about 1.3 wt% of CO, about 79 wt% of CO2, about 1 wt% of Nhh, and about 1.9 wt% of hhS. [0084] In another exemplary embodiment, the bioreactor feed may comprise about 11.5 wt% of H2, about 6 wt% of CO, about 73 wt% of CO2, about 2.5 wt% of NH3, and about 4.7 wt% of H2S.

[0085] The bioreactor feed may enter the bioreactor through one or more inlets, as one or more streams. In one embodiment, at least two of the components of the gaseous mixture may be mixed before entering the bioreactor. In another embodiment, at least three of the components may be mixed before entering the bioreactor. In an alternate embodiment, the components of the gaseous mixture may separately enter the bioreactor, i.e. , the components of the gaseous mixture are not mixed before entering the bioreactor. In each of the above embodiments, the nitrogen source and/or the sulfur source may or may not be mixed with the components of the gaseous mixture before entering the bioreactor. For instance, in one embodiment, the gaseous mixture and the nitrogen source may be mixed together before entering the bioreactor. In another embodiment, the gaseous mixture and the nitrogen source may not be mixed together before entering the bioreactor. In another embodiment, a sulfur source may be added to the bioreactor. In still another embodiment, at least two of the gaseous mixture, the nitrogen source, and the sulfur source may be mixed together before entering the bioreactor. For instance, the gaseous mixture comprising H2 and CO, CO2, or CO and C02 and the nitrogen source may be mixed before entering the bioreactor. Alternatively, the gaseous mixture comprising H2 and CO, CO2, or CO and C02 and the sulfur source may be mixed before entering the bioreactor. In another example, the nitrogen source and the sulfur source may be mixed before entering the bioreactor. In still another example, two independent streams comprising the gaseous mixture may be mixed before entering the bioreactor. In another embodiment, the gaseous mixture, the nitrogen source, and the sulfur source may be mixed together before entering the bioreactor.

Bioreactor conditions

[0086] The bioreactor contains an aqueous mixture comprising hydrogenotrophic microorganisms and fermentation medium. As used herein, the term “fermentation media” refers to the input media and“fermentation broth” refers to the output media. Stated another way, fermentation broth is fermentation media that has changed as a result of fermentation, for instance by depletion of certain media

components and/or addition of metabolic products produced during fermentation. Media compositions for culturing hydrogenotrophic microorganisms are known in the art. In general, such media comprise de-aerated water, nutrients, salts, vitamins, and/or minerals. The hydrogenotrophic microorganisms may be grown by batch culture, fed- batch culture, or continuous culture methodologies.

[0087] A classic batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to external alterations during the culture process. Thus, at the beginning of the culturing process, the media is inoculated with the desired hydrogenotrophic microorganism (e.g., methanogen) and growth or metabolic activity is permitted to occur without adding anything to the system. Generally, a "batch" culture is batch with respect to the addition of carbon source, gas feedstock and media components, wherein waste gasses are allowed to exit, and attempts are often made at controlling other factors, such as pH. In batch systems, the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures, cells pass through a static lag phase to a high growth logarithmic phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in logarithmic growth phase are often responsible for the bulk production of end product or intermediate in some systems. Stationary or post exponential phase production can be obtained in other systems.

[0088] A fed-batch system is a variation on the standard batch system. Fed-batch culture processes comprise a batch system with the modification that substrate and potentially media components are added in increments as the culture progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. In gas substrate fermentations, a system is continuous with respect to gas substrate (since waste gas can be removed) and fed-batch with respect to liquid (media). Batch and fed-batch culturing methods are common and known in the art (see, e.g., Thomas D. Brock, Biotechnology: A Textbook of Industrial Microbiology, 2nd Ed. (1989) Sinauer Associates, Inc., Sunderland, Mass.; Deshpande, Appl.

Biochem. Biotechnol. 36:227, 1992.

[0089] Continuous cultures are "open" systems where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously (with or without biomass or cell retention) for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in logarithmic phase growth, though cells may also be in stationary phase. Continuous culture may involve biomass, cell retention or cell immobilization where feedstock and nutrients are continuously added and valuable products, by-products, and waste products can be continuously removed from the cell mass. Cell retention may be performed by a variety of methods, such as by filtration, centrifugation or settling. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials.

[0090] Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method can maintain a limited nutrient (e.g., carbon source, nitrogen level, hydrogen level, phosphorous level) at a fixed rate and allow all other parameters to modulate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. In certain embodiments, hydrogenotrophic biomass growth is limited to increase product to biomass ratio. Methods of modulating nutrients and growth factors for continuous culture processes, as well as techniques for maximizing the rate of product formation, are well known in the art (see Brock, 1989).

[0091 ] In general, the concentration of the hydrogenotrophic

microorganisms in the bioreactor may range from about 1 g/L to about 100 g/L. In various embodiments, the concentration of the hydrogenotrophic microorganisms may ranges from about 2 g/L to about 50 g/L. In other embodiments, the concentration of the hydrogenotrophic microorganism may be about 4g/L, about 10 g/L, about 15 g/L, about 20 g/L, about 25 g/L, about 30 g/L, about 35 g/L, about 40 g/L, or about 45 g/L

[0092] The pressure inside the bioreactor generally is greater than about 1 bar absolute. In various embodiments, the pressure in the bioreactor may be greater than 1 , 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 bar absolute. In other embodiments, the pressure in the bioreactor may be greater than about 100, about 200, about 300, about 400, about 600, about 700, about 800, about 900 or about 1000 bar absolute. In certain embodiments, the pressure may be between about 1 bar absolute and about 5 bar absolute; between about 1 bar absolute and about 10 bar absolute; between about 2 bar absolute and about 10 bar absolute; between about 3 bar absolute and about 10 bar absolute, between about 4 bar absolute and about 10 bar absolute, or between about 5 bar absolute and about 10 bar absolute.

[0093] The temperature inside the bioreactor may range from about 25 °C to about 85 °C. In various embodiments, the temperature in the bioreactor may range from about 25 °C to about 35 °C, from about 35 °C to about 45 °C, from about 45 °C to about 55 °C, from about 55 °C to about 65 °C, from about 65 °C to about 75 °C, or from about 75 °C to about 85 °C. In one embodiment, the temperature in the bioreactor may be about 35-37 °C. In another embodiment the temperature in the bioreactor may be about 65 °C. The fermentation process may be exothermic, and heat may need to be removed from the bioreactor using techniques well known in the art.

[0094] The pH of the aqueous mixture in the bioreactor may range from about 6.5 to about 7.5. In various embodiments, the pH may be about 6.5, about 6.6, about 6.7, about 6.8, about 6.9, about 7.0, about 7.1 , about 7.2, about 7.3, about 7.4, or about 7.5. The CO2 in the gaseous mixture may act as a buffer and help maintain the pH at the desired level. While the oxygen content in the reactor generally is minimized, up to 400 ppm may be present.

[0095] Many methods are available to stir, mix, or agitate the contents of the bioreactor and/or provide increased gas absorption into the aqueous mixture.

Stirring provides a high concentration of the gaseous substrates in the aqueous mixture. In various embodiments, these methods simply mix the aqueous mixture. In other embodiments, the method not only mixes the aqueous mixture but also provides increased of gas absorption of various components of the gaseous mixture into the aqueous mixture.

[0096] Non-limiting methods of stirring the aqueous mixture include jet stirring, impellers, baffles, or combinations thereof. Non-limiting examples of methods to mix the contents of the bioreactor and provide increased gas absorption into the aqueous mixture include jet stirring using at least one eductor, jet stirring comprising at least one nozzle and at least one eductor, jet stirring wherein jet stirring comprises at least one nozzle is directed through the gas phase into the aqueous mixture, specially designed impellers that create adequate gas absorption into the aqueous mixture, bioreactors with specially designed baffles, and combinations thereof. A non-limiting example of a method to provide increased absorption of the gas into the aqueous mixture is a spray nozzle, wherein a portion of liquid from the aqueous mixture is pumped through the spray nozzle into the gas resulting in absorption of the gas into the spray of the aqueous mixture. In one embodiment, the bioreactor comprises a spray tower to facilitate mixing and absorption of gas into the aqueous mixture.

[0097] Jet mixing utilizing at least one nozzle withdraws a liquid portion of the aqueous mixture from the bioreactor and pumps the liquid back into the bioreactor through at least one nozzle. This creates turbulence in the aqueous mixture and increases mixing. The at least one nozzle may be positioned below the surface of the aqueous mixture, at the surface of the aqueous mixture, or directed through the gas phase into the aqueous mixture.

[0098] Jet mixing, utilizing at least one eductor, withdraws a liquid portion of the aqueous mixture from the bioreactor and pumps the liquid back into the

bioreactor through at least one gas educting nozzle. The eductor nozzle provides suction in the eductor which pulls gas, mixes the gas with the circulated aqueous mixture, and returns the resulting back into the bioreactor, where the aqueous mixture has increased absorption of the gas as compared to the circulated aqueous mixture. When the flow from the eductor nozzle is directed towards the aqueous mixture, increased gas absorption of the gas in the aqueous mixture and increased turbulence of the aqueous mixture result.

[0099] Jet mixing may also utilize at least one nozzle and at least one eductor. In this configuration, as described above, not only increased turbulence in the aqueous mixture, but also increased gas absorption of the gas into the aqueous mixture may be realized. [00100] The use of a spray nozzle may also be utilized. Using a spray nozzle, a liquid portion of the aqueous mixture is pumped through the spray nozzle producing droplets of the liquid. These droplets may be discharged into the gas, where they absorb at least some of the gas. The droplets are then reincorporated into the aqueous mixture, thereby increasing the amount of gas dissolved in the aqueous mixture.

[00101 ] In other embodiments, a draft tube may be utilized in the process. The draft tube is located within the bioreactor, and provides an internal recirculation of the aqueous mixture within the bioreactor. The circulation may be induced by energy from the at least one liquid jets, from the at least one gas educting nozzle, from rising gas bubbles within the bioreactor, or a combination thereof.

[00102] If desired, one or more of the methods described above may be utilized in the processes disclosed herein. The various mixing methods may create foam in the bioreactor. The foam may be reduced via the use of chemical foam breakers (e.g., surfactants, etc.) and/or mechanical foam breakers (e.g., separators, spray nozzle, etc.).

[00103] The hydrogenotrophic microorganisms in the bioreactor convert the gaseous mixture comprising H2, COx, and optionally Nhh or H2S into at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid or its conjugate base, or a hydroxyl or keto acid.

[00104] In some embodiments, at least one fermentation product may be an amino acid. Any amino acid may be produced by the processes disclosed herein including standard amino acids and non-standard amino acids in either or both the D- or L-form. As a non-limiting example, the amino acid may be 2-aminobutyrate, alanine, beta-alanine, arginine, aspartate, carnitine, citruline, cystine, dehydroalanine, glutamate, glutamine, glycine, hydroxyproline, isoleucine, leucine, lysine, methionine, ornithine, phenylalanine, proline, pyroglutamate, pyrroproline, selenocysteine, selenomethionine, serine, threonine, tryptophan, tyramine, tyrosine, valine, or any combination thereof. As another non-limiting example, the amino acid may be glycine, lysine, methionine, threonine, or any combination thereof. In a specific embodiment, at least one

fermentation product may be methionine. In another specific embodiment, at least one fermentation product may be a seleno amino acid. In another specific embodiment, at least one fermentation product may be a seleno amino acid and methionine.

[00105] In some embodiments, at least one fermentation product may be an alcohol, aldehyde or a ketone. As a non-limiting example, the alcohol, aldehyde or ketone may be acetone, butanol, ethanol, glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

[00106] In some embodiments, at least one fermentation product may be a carboxylic acid or a conjugate base of a carboxylic acid. The term“carboxylic acid,” as used herein, is understood to include the conjugate base unless otherwise specified. As a non-limiting example, the carboxylic acid may be acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, succinate, or any combination thereof.

As another non-limiting example, the carboxylic acid may be fumarate or succinate. As another non-limiting example, the carboxylic acid may be acetate, butyrate, formate, isobutyrate, isovalerate, malonate or propionate.

[00107] In some embodiments, at least one fermentation product may be a hydroxy acid or a keto acid. As a non-limiting example, the hydroxy acid or keto acid may be 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, pyruvate, or any combination thereof. As another non-limiting example, the hydroxy acid or keto acid may be 2- hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2-hydroxyvalerate, 2- hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3-hydroxyisovalerate, 3-methyl-2-oxovalerate, or any combination thereof. As another non-limiting example, the hydroxy acid or keto acid may be 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2- hydroxyisovalerate, 2-hydroxyvalerate, 3-hydroxybutyrate, 3-hydroxyisovalerate, acetate, or any combination thereof. As another non-limiting example, the hydroxy acid or keto acid may be 4 hydroxybenzoate, 4-hydroxyphenyllactate, or a combination thereof.

[00108] In one embodiment, at least one of the following reactions occurs in the bioreactor:

[00109] It is understood that C5H11NO2S is the amino acid, methionine. As shown above, in some embodiments, methionine is formed when the hydrogenotrophic microorganisms convert at least some of the gaseous mixture into one or more fermentation products. In such instances, the gaseous mixture fed to the bioreactor comprises H2, COx, NH3, and H2S, where x is 1 and/or 2.

[00110] In embodiments in which the desired fermentation product is one or more amino acids, the processes disclosed herein may produce said one or more amino acids at about 0.001 g/L of culture to about 500 g/L of culture. In some embodiments, the amount of one or more amino acids produced is about 1 g/L of culture to about 100 g/L of culture. In further embodiments, the amount of one or more amino acids produced is about 0.001 g/L, 0.01 g/L, 0.025 g/L, 0.05 g/L, 0.1 g/L, 0.15 g/L, 0.2 g/L, 0.25 g/L, 0.3 g/L, 0.4 g/L, 0.5 g/L, 0.6 g/L, 0.7 g/L, 0.8 g/L, 0.9 g/L, 1 g/L,

2.5 g/L, 5 g/L, 7.5 g/L, 10 g/L, 12.5 g/L, 15 g/L, 20 g/L, 25 g/L, 30 g/L, 35 g/L, 40 g/L, 45 g/L, 50 g/L, 60 g/L, 70 g/L, 80 g/L, 90 g/L, 100 g/L, 125 g/L, 150 g/L, 175 g/L, 200 g/L, 225 g/L, 250 g/L, 275 g/L, 300 g/L, 325 g/L, 350 g/L, 375 g/L, 400 g/L, 425 g/L, 450 g/L, 475 g/L, or 500 g/L.

[00111 ] In some embodiments, the fermentation processes produce ChU, which can be used in the processes disclosed herein to 1 ) generate heat, 2) be converted into products such as COx and H2, 3) be sent to a different process, and/or 4) be discarded.

(c) Removing a gas stream from the bioreactor

[00112] The process further comprises removing a gas stream from the bioreactor, the gas stream comprising at least H2 and COx, where x is 1 and/or 2. In some embodiments, the gas stream comprises a combination of at least three or at least four of H2, H2S, Nhh, CO, CO2, ChU, and water vapor. In some embodiments, the gas stream further comprises ChU. In other embodiments, the gas stream further comprises H2S. [00113] The gas stream that is removed may be used as is, or may be passed through one or more devices as needed to process the gas stream and/or to divide the gas stream into multiple portions. When the gas stream is divided into multiple portions and processing occurs, processing may occur before and/or after division. In embodiments, when processing occurs after division into multiple portions, each portion may be processed the same or differently. Processing may involve passing the gas stream or portion thereof through a separation device, creating a depleted gas stream and a separated gas stream. In some embodiments, multiple separation devices may be used in series or in parallel, creating a plurality of depleted and separated gases. Alternatively, or in addition, processing may involve adding one or more component to the gas stream, a depleted gas stream, or a portion thereof, creating a conditioned gas stream. Some or all of the gas stream, a depleted gas stream, a separated gas stream, and/or a conditioned gas stream may then be used elsewhere in the process, used in a different process, vented, or combusted to generate heat for the process disclosed herein or for another process. If the gas stream, a depleted gas stream, a separated gas stream, and/or a conditioned gas stream is to be combusted, it may be mixed with other gases, such as methane, syngas and/or oxygen. In embodiments where some or all of the gas stream, a depleted gas stream, a separated gas stream, and/or a conditioned gas stream is used in the process disclosed herein, the gas may be recycled back to one or both of the one or more reactors or the bioreactor. In some embodiments, some or all of the gas stream, a depleted gas stream, a separated gas stream, and/or a conditioned gas stream may be pressurized by passage through a gas compressor prior to being recycled back to one or both of the one or more reactors or the bioreactor.

[00114] In some embodiments, at least 50% of the gas stream removed from the bioreactor is recycled back to one or both of the one or more reactors or the bioreactor. For instance, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the gas stream removed from the bioreactor may be recycled. In some embodiments, about 50% to about 70% of the gas stream removed from the bioreactor is recycled back to one or both of the one or more reactors or the bioreactor. In some embodiments, about 60% to about 80% of the gas stream removed from the bioreactor is recycled back to one or both of the one or more reactors or the bioreactor. In some embodiments, about 70% to about 90% of the gas stream removed from the bioreactor is recycled back to one or both of the one or more reactors or the bioreactor. In some embodiments, about 80% to about 100% of the gas stream removed from the bioreactor is recycled back to one or both of the one or more reactors or the bioreactor. In an exemplary embodiment, about 70% to about 100%, or about 75% to about 95%, is recycled back to one or both of the one or more reactors or the bioreactor and the remainder is combusted.

[00115] In certain embodiments above, the gas stream, or portion thereof, is processed before being recycled back to the one or more reactors and/or the bioreactor. For example, the gas stream, or portion thereof, may enter one or more separation devices, wherein each separation device at least partially removes at least one component of the gas stream, thereby creating a depleted gas stream and a separated gas stream. Certain separation devices are designed to remove two or more components. Thus, when the gas stream enters a separation device, the concentration of one or more components is reduced, relative to the concentration of the

component(s) in the gas stream. This resulting material, having a lower concentration of at least one component, is the depleted gas stream. In some embodiments, at least some of the depleted gas stream enters a second separation device. If desired, additional separation devices, such as third, fourth and/or fifth separation devices may be used. If more than one separation device is used, the separation devices are connected in series. Alternatively, they are connected in parallel. Typically, the first, second and any subsequent separation devices remove a different component. For example, if the first separation device removes H2S, the second separation device is typically designed to remove a different compound that is not H2S. But if purity requirements necessitate it, two or more separation devices may be used to remove or reduce the concentration of the same component. The separated gas stream(s) comprising component(s) removed from the gas stream and/or a depleted gas stream may be recycled to the one or more reactors or the bioreactor, combusted, used elsewhere in the process, used in a different process, purged, or any combination thereof. In some embodiments, some or all of a depleted gas stream and/or a separated gas stream may be pressurized by passage through a gas compressor prior to being recycled back to one or both of the one or more reactors or the bioreactor.

[00116] In one example, at least some H2S is removed from the gas stream in a separation device referred to herein as an“H2S separation device” or an“H2S scrubber”. Although not required, H2S is typically removed from a gas stream first, before other components are removed or utilized. As such, an H2S separation device, when present, is typically the first separation device. Suitable H2S separation devices may use any H2S removal technology known in the art. As a non-limiting example, the H2S separation device may contain a catalyst that catalytically oxidizes H2S to S. In another non-limiting example, the H2S separation device may contain a metal compound that is irreversibly converted by reaction with H2S. For instance, the metal compound may be a metal oxide such as zinc oxide or iron oxide. In one embodiment, the H2S separation device comprises zinc oxide and the following reaction occurs within the H2S separation device:

In another non-limiting example, the H2S separation device may be an amine scrubber. Amine scrubbers will remove both H2S and CO2. In another non-limiting example, the H2S separation device may be a non-amine technology. A variety of non-amine technologies are being developed to reduce fouling that may occur with amine based H2S removal. In one embodiment, a non-amine H2S separation device is potassium carbonate scrubber, however, other non-amine technologies may also be used.

Preferably at least some of the H2S is removed from the gas stream. More preferably, all H2S or at least 95% of the H2S is removed from the gas stream. In some

embodiments, two or more H2S separation devices are used in series to remove at least 95% of the H2S. For instance, the gas stream or portion thereof may enter a first H2S separation device (e.g., an amine scrubber, a potassium carbonate scrubber, a ZnO scrubber, etc.) and a depleted gas stream having a reduced concentration of H2S (as compared to the gas stream entering the first H2S separation device) may exit the first H2S separation device and enter a second H2S separation device (e.g., an amine scrubber, a potassium carbonate scrubber, a ZnO scrubber, etc.), and then a residual gas stream having a reduced concentration of H2S (as compared to the depleted gas stream) may exit the second H2S separation device. The first and second H2S separation device may use the same or different H2S removal technology. In one embodiment, the first H2S separation device is an amine scrubber or a potassium carbonate scrubber, and the second H2S separation device is a ZnO scrubber. In further embodiments, one or more additional separation devices may be used to remove one or more further components from the H2S depleted or residual gas stream, or a portion thereof. Alternatively, or in addition, at least some of the depleted or residual gas stream is burned or otherwise oxidized to generate heat, which can be used in the processes disclosed herein and/or used in another process. Alternatively, or in addition, at least some of the H2S depleted or residual gas stream may be recycled back to one or both of the one or more reactors or the bioreactor. Some or all of the separated gas stream comprising H2S may be recycled back to the bioreactor.

[001 17] In another example, at least some CO2 is removed from the gas stream, depleted gas stream, or a portion thereof, in a separation device referred to herein as a“CO2 separation device” or a“CO2 scrubber.” The separation device removes at least some CO2 and thereby affords a separated gas stream comprising CO2 and a residual gas stream, wherein the residual gas stream has a reduced concentration of CO2, relative to the material that entered the CO2 separation device. Suitable CO2 scrubbers may use any CO2 removal technology known in the art. As a non-limiting example, a CO2 scrubber may be an amine scrubber. Amine scrubbers will remove both H2S and CO2, as such, a single separation device may be used to reduce the concentration of both H2S and CO2. In further embodiments, one or more additional separation devices may be used to remove one or more further components from the CO2 depleted gas stream, or a portion thereof. Alternatively, or in addition, at least some of the CO2 depleted gas stream is burned or otherwise oxidized to generate heat, which can be used in the processes disclosed herein and/or used in another process. Alternatively, or in addition, at least some of the CO2 depleted gas stream may be recycled back to one or both of the one or more reactors. Some or all of the separated gas stream comprising CO2 may be vented and/or recycled back to the bioreactor.

[001 18] In another example, at least some H2 is removed from the gas stream, a depleted or residual gas stream, or a portion thereof, in a separation device referred to herein as an“hte separation device”. The separation device removes at least some H2 and thereby affords a separated gas stream comprising H2 and a residual gas stream, wherein the residual gas stream has a reduced concentration of H2, relative to the material that entered the H2 separation device. In an embodiment, at least 50 % by weight of the H2 is removed. All or some of the removed H2 can be converted into H2S and/or can be combusted to generate heat. The heat can be used in the processes disclosed herein or it can be used in a different process. If it is to be combusted, it may be mixed with other gases, such as methane, syngas and/or oxygen. In some embodiments, the residual gas stream further comprises at least one of ChU, CO and/or CO2. In a further embodiment, it comprises ChU and at least one of CO or CO2. In an embodiment, the H2 separation device comprises a pressure swing adsorption unit or a hydrogen membrane. In one preferred embodiment, the second separation device is a hydrogen membrane. The hydrogen membrane may comprise a palladium membrane, a ceramic membrane or a combination thereof. The H2 that is removed is at least 80% pure, at least 85% pure, at least 90% pure or at least 95% pure, by weight.

[00119] In still further embodiments, each bioreactor has one or more separation devices that are dedicated to it. Thus, if four bioreactors are used, at least four separation devices will be used. Alternatively, the gas streams leaving more than one bioreactor can be combined and then the combined gas stream can enter a single separation device. An advantage of this process is that it is more cost effective, because fewer separation devices are needed. A possible drawback of combining the gas stream is the risk of a bioreactor contaminating one or more other bioreactors. To help minimize this risk, the bioreactors may be equipped with one way valves to prevent the gas stream from one bioreactor entering and possibly contaminating another bioreactor.

(d) Removing a liquid stream from the bioreactor

[00120] The process further comprises removing a liquid stream from the bioreactor, the liquid stream comprising fermentation broth comprising at least one fermentation product and hydrogenotrophic microorganisms. In a continuous process, some fermentation broth and cell mass is removed. In a batch process, all of the fermentation broth and cell mass is removed.

[00121 ] The liquid stream is passed through a separator that separates some or all of the cell mass from an amount of the fermentation broth. Generally, the portion of the liquid stream that remains (also referred to herein as“the retentate”) comprises a concentrated amount of cell mass (e.g. hydrogenotrophic microorganisms) and the portion of the liquid stream that is separated off (also referred to herein as“the filtrate,” even when the separation technique is not filtration) comprises a reduced amount of cell mass and at least one fermentation product. Preferably, the filtrate is substantially free of intact cells.

[00122] Various methods can be used to separate cell mass from liquids, including but not limited to filtration, centrifugation, chromatography, precipitation, and the like. In an embodiment, the liquid stream is centrifuged, thereby creating a filtrate and a retentate. In another embodiment, the liquid stream is filtered, thereby creating a filtrate and a retentate. Various methods can be used to filter the liquid stream, such as gravity filtration, vacuum filtration, and pressure filtration. More specific examples of methods include microfiltration, ultrafiltration, and reverse osmosis.

[00123] In some embodiments, two or more separation steps may be used. For instance, a filtration method can be used first, followed by at least one other filtration method and/or at least one other separation method. As an example, gravity filtration followed by microfiltration can be used, or vacuum filtration followed by centrifugal separation can be used. Or, vacuum filtration to remove larger particles, followed by microfiltration to remove smaller particles. Alternatively, centrifugal separation can be used first, followed by at least one other separation method. In another example, chromatography can be used first, followed by at least one other separation method.

[00124] In a specific embodiment, the liquid stream is filtered using microfiltration. In another embodiment, microfiltration is used in combination with at least one other separation method.

[00125] In each of the above embodiments, the liquid stream and/or the filtrate may also be heated prior to a separation step, which facilitates the dissolution of the fermentation products in the fermentation broth and their separation from the hydrogenotrophic microorganisms and/or other solids.

[00126] All or part of the retentate comprising hydrogenotrophic

microorganisms and fermentation broth can be recycled back to the bioreactor or it can be discarded. In an embodiment, at least some of the retentate may be recycled back to the bioreactor. In one embodiment, about 1 % to about 3% by weight of the retentate is removed as purge prior to recycling the remainder of the retentate back to the bioreactor. If any retentate is recycled back to the bioreactor, it may be combined with fermentation medium or any component thereof, or with recycled water, to form a recycle stream that is recycled back to the bioreactor. Further, fresh hydrogenotrophic microorganism(s) may be added to the recycle stream. Inactive hydrogenotrophic microorganisms may also be removed before the retentate is recycled back to the bioreactor.

(e) Purifying the fermentation product

[00127] The filtrate, which comprises dissolved gases and the one or more fermentation products (among other things), is then treated to thereby isolate at least some of the one or more fermentation products. The one or more fermentation products may be purified by a process chosen from filtration, chromatography, crystallization, solvent extraction, centrifugation, dialysis, drying, precipitation, phase separation, or combinations thereof. Non-limiting examples of suitable types of filtration include microfiltration, ultrafiltration, and reverse osmosis. Non-limiting examples of suitable types of chromatography include affinity chromatography, size exclusion chromatography, adsorption chromatography, and hydrophobic interaction

chromatography. A non-limiting example of a suitable type of centrifugation includes ultracentrifugation. Non-limiting examples of suitable types of drying include

evaporation, freeze drying, spray drying, vacuum drying, etc. In some embodiments, one or more fermentation products are purified by a process chosen from microfiltration, ion exchange chromatography, evaporation, crystallization, or a combination thereof. In some embodiments, the purification process may further comprise affinity

chromatography, size exclusion chromatography, adsorption chromatography, hydrophobic interaction chromatography, centrifugation, ultracentrifugation, precipitation, immunoprecipitation, solvent extraction, dialysis, drying, phase separation, and the like. As part of the process to purify the one or more fermentation products, the filtrate (or treated filtrate when multiple methods are used) may be de-gassed. Many of the processes that may be used to purify the one or more fermentation products will also degas, including evaporation, spray-drying and the like.

[00128] During purification, the removal of one or more fermentation products from the filtrate results in the production of a fermentation product depleted filtrate fraction. All or a portion of fermentation product depleted filtrate fraction may be recycled back to the bioreactor, and in preferred embodiments the recycled stream will be sterilized before entering the bioreactor. The fermentation product depleted filtrate fraction may also be combined with recycled water and/or de-gassed before being recycled back to the bioreactor. Alternatively, an aqueous composition may be removed from the fermentation product depleted filtrate fraction and the aqueous composition may be recycled back to the one or more reactors or the bioreactor, and in preferred embodiments the recycled composition will be sterilized before entering the one or more reactors or the bioreactor. The aqueous composition may also be combined with recycled water and/or de-gassed before being recycled back to the bioreactor.

[00129] In some embodiments, the filtrate fraction may be subjected to ion exchange chromatography in a manner such that at least one impurity is retained on the ion exchange media thereby separating the at least one impurity from the one or more fermentation products in the filtrate fraction. The ion exchange media may be anionic exchange media or cationic exchange media. The filtrate fraction containing the one or more fermentation products is then subjected to one or more additional purification methods to isolate one or more fermentation products.

[00130] In other embodiments, the filtrate fraction may be subjected to ion exchange chromatography in a manner such that one or more fermentation product is retained on the ion exchange media thereby separating the one or more fermentation products from other components in the filtrate fraction. The one or more fermentation products may be eluted from the ion exchange media and optionally subjected to one or more additional purification methods to isolate one or more fermentation products.

[00131 ] The filtrate, or a fraction of the filtrate following ion exchange chromatography or other purification process, comprising one or more fermentation products may enter a concentrator, wherein the one or more fermentation products are concentrated to form a concentrated fraction and water is removed forming a depleted filtrate (see, e.g., Figure 10). In some embodiments, the concentrator is an evaporator. The evaporation may be conducted at a temperature of about 100 °C to about 140 °C, e.g., at about 100°C, at about 110°C, at about 120°C, at about 130°C, at about 140°C, etc. In an exemplary embodiment, evaporation may occur at about at about 120°C.

The one or more fermentation products may be concentrated to an amount of about 10% by weight to about 20% by of the filtrate or filtrate fraction, e.g., to about 14% by weight.

[00132] In some embodiments, the concentrated fraction comprising one or more fermentation products may then enter a crystallizer such that one or more fermentation products can form crystals. The crystallizer may be a forced circulation crystallizer. The crystallization procedure may be conducted under vacuum. In certain embodiments, the concentrated fraction comprising one or more fermentation products may be cooled to a temperature of about 25° to about 30° C resulting in formation of crystals of the one or more fermentation products. The crystals of the one or more fermentation products may be isolated via centrifugation. In some embodiments, the crystals of the one or more fermentation products may have a moisture content of less than about 30% by weight, less than about 20% by weight, or less than about 10% by weight.

[00133] In further embodiments, the crystals of the one or more

fermentation products may then be dried. The drying may be accomplished using fluidized dryer system. The fluid bed may be a shaking fluid bed or a static fluid bed. In general, the temperature of the drying process does not exceed about 100 °C. In some embodiments, the temperature of the drying process does not exceed about 90 °C. In some embodiments, the temperature of the drying process does not exceed about 80 °C. In some embodiments, the temperature of the drying process does not exceed about 70 °C. In some embodiments, the temperature of the drying process does not exceed about 60 °C. In some embodiments, the temperature of the drying process may range from about 30 °C to about 100 °C, or from about 40 °C to about 100 °C, or from about 50 °C to about 100 °C. In some embodiments, the temperature of the drying process may range from about 30 °C to about 90 °C, or from about 40 °C to about 90 °C, or from about 50 °C to about 90 °C. In some embodiments, the temperature of the drying process may range from about 30 °C to about 80 °C, or from about 40 °C to about 80 °C, or from about 50 °C to about 80 °C. In some embodiments, the temperature of the drying process may range from about 30 °C to about 70 °C, or from about 40 °C to about 70 °C, or from about 50 °C to about 70 °C. In some embodiments, the temperature of the drying process may range from about 30 °C to about 60 °C, or from about 40 °C to about 60 °C, or from about 50 °C to about 60 °C. The drying process may proceed until the crystals of the one or more fermentation products have a moisture content of less than about 1 % by weight.

[00134] The water removed during the evaporation process, the

crystallization process, and/or during the drying process may be recycled back into the overall process at one or more places. For instance, water may be recycled to the one or more reactors, to the bioreactor, to be combined with recycled cell mass, to be combined with to a fermentation product depleted filtrate fraction (or fraction thereof). Alternatively, or in addition, water removed during the process may be sent to a clean water hold tank prior to being recycled back into the process. The water may be de gassed prior to being recycled or sent to the clean water hold tank. Water removed during the process and recycled back into the process may contain minor impurities.

[00135] The yield of the one or more fermentation products can and will vary depending on the amounts of starting substrates fed to the bioreactor, the concentration of the hydrogenotrophic microorganisms in the bioreactor, and the identity of the fermentation product. In embodiments in which the desired fermentation product is one or more amino acids, the processes disclosed herein may produce at least about or up to about 1 kilogram (kg), at least about or up to 10 kg, at least about or up to 100 kg, at least about or up to 1 ,000 kg, at least about or up to 10,000 kg, at least about or up to 50,000 kg, at least about or up to 100,000 kg, at least about or up to 250,000 kg, at least about or up to 500,000 kg, or more of amino acid/day. In certain embodiments, one or more amino acids is produced at about 100,000 metric tons (MT) per year (i.e. ,

100 million kg per year or 300,000 kg/day), about 75,000 MT per year (or 225,000 kg/day), about 50,000 MT per year (or 150,000 kg/day), about 25,000 MT (or 75,000 kg/day), or about 10,000 MT per year (or 30,000 kg/day).

(f) Additional Embodiments

[00136] Figure 1 shows one possible arrangement of a reactor, bioreactor, and separation devices that can be used in the process 100 to produce at least one fermentation product. An organic substrate, e.g., methane (CFU) 105 and process steam are introduced into a reactor 110, where the organic substrate is converted to a gas mixture containing hydrogen gas (H2), carbon monoxide (CO) and/or carbon dioxide (CO2), which is commonly referred to as syngas. The methane 105 may be natural gas or otherwise generated from a bioreactor, industrial process or other reactor, as described herein. Although not shown here, the source of methane may be conditioned to adjust the concentration of the components contained therein. For example, when natural gas is the methane source, the natural gas feed may contain CO2 and H2S concentrations deleterious to steam methane reforming. Accordingly, the natural gas feed may be conditioned by removing or reducing CO2 and H2S to a desired amount (e.g., < 15 ppmv, <10 ppmv, <5 ppmv, or less). Alternatively, or in addition, the natural gas feed may be conditioned to remove or reduce FICN, COS, and/or other impurities that may be deleterious to the bioreactor. In the embodiment depicted by Figure 1 , two reactions occur in reactor 110, i.e., a steam methane reforming reaction and a water gas shift reaction. In other embodiments, not shown, the steam methane reforming reaction occurs in one reactor, while the water gas shift reaction occurs in a different reactor (see, e.g., Figure 6). The gas mixture leaves the reactor 110 and specific gases can be removed and/or additional gases can be added. For example, the gas mixture can be passed through a separation device to remove H2, which can be used in other processes (e.g., H2S forming reactions), as fuel for a steam methane reformer reactor, or can be purged (see, e.g., Figure 9). As shown in Figure 1 , nitrogen and optional sulfur sources can be added. For example, a nitrogen source, NH3, and a sulfur source, H2S, may be added to the gas mixture, before it enters the bioreactor 115. While not shown, the NH3 and H2S may be combined and then added to the gas mixture in a single stream. When the Nhh and H2S are added to the gas stream, nozzles or other mixing devices may be used to ensure mixing of the Nhh and hhS into the gas stream.

In one embodiment, baffles may be used alone or in combination with one or more other mixing devices. In other embodiments, not shown, one or more of the other gases are not mixed into the gas mixture and instead, they are introduced directly into the bioreactor 115.

[00137] The bioreactor 115 contains an aqueous mixture comprising hydrogenotrophic microorganisms that convert at least some of the gases introduced into bioreactor 115 into one or more fermentation products. Once the desired amount of product is generated, a liquid stream comprising the hydrogenotrophic microorganisms and the one or more fermentation products is removed from the bioreactor 115. As shown in Figure 1 , the liquid stream enters a separator 140, which separates some or all of the solids from an amount of the fermentation broth. The portion of the liquid stream from which some or all of the solids is removed (i.e. , the filtrate) is substantially is free of intact cells (e.g., hydrogenotrophic microorganisms) and the remainder of the liquid stream (i.e., the retentate) comprises a concentrated amount of hydrogenotrophic microorganisms.. The retentate may be recycled to the bioreactor 115, it may be used elsewhere in the process, and/ or it may be discarded. Although not shown here, two or more separators may be used in series to successively decrease the solid content of the filtrate. The filtrate, which comprises one or more fermentation products and dissolved gases, then enters a concentrator 145, which reduces the water content of the filtrate. The concentrated filtrate is then sent for further purification and the one or more fermentation product is isolated. The liquid removed from the filtrate by the

concentrator 145 is referred to as the depleted filtrate and may be recycled to the bioreactor 115 and/or be used in other parts of the process. The liquid generated upon purifying the fermentation product(s), or fractions thereof, may be recycled to the bioreactor 115, the starter reactor 135, mixed with the recycled retentate, used in other parts of the process and/or discarded. [00138] Starter reactor 135 is used to grow the hydrogenotrophic microorganisms used in bioreactor 115. While only one starter reactor 135 is shown in Figure 1, if desired, more than one starter reactor 135 may be used, either in series or in parallel. Liquid and microorganism from starter reactor 135 is used to initially inoculate a bioreactor (e.g. a new bioreactor, a cleaned and refilled bioreactor, etc.). Typically microorganism growth in in bioreactor 115, and optional cell mass recycle through retentate recycling, is sufficient to make up for any loss in the liquid stream removed from the bioreactor 115. If however needed at any point in operation the liquid and microorganism content in the bioreactor 115 may be replenished by introducing liquid and microorganism from the starter reactor 135.

[00139] The gas stream leaving the bioreactor 115 enters a separation device 120, such as an FteS separation device before it enters an optional second separation device 125, such as a H2 separator, where at least some H2 is removed, generating a residual gas stream. Although not shown here, H2S separation device 120 may remove one or more components in addition to H2S, for example CO2, and the optional second separation device may remove a component of the gas stream other than H2. In addition, while Figure 1 shows only two separation devices, it should be understand that 3, 4, 5 or any number of separation devices may also be used. The residual gas stream leaving the second separation device 125 enters a compressor 130, where the pressure of the residual gas stream is increased. The pressurized, residual gas stream is then combined with a methane source and recycled to the reactor 110. If desired, the residual gas stream is not mixed with a methane source but is sent directly to the reactor 110. Additional separation devices, not shown, may be used to further condition the gas stream before it is recycled to the reactor 110.

[00140] Figure 2 illustrates an alternate arrangement of components that may be used to effect process 100, wherein multiple bioreactors are used in parallel. While Figure 2 shows four bioreactors in parallel, it should be understood that 2, 3, 4, 5, 6 or any number of bioreactors and related components may be used. As in Figure 1 , starter bioreactor 135 feeds microorganism containing broth to bioreactor 115, where the microorganisms convert the gases from reactor 110, NH3, and optionally H2S to one or more fermentation products. As in Figure 1 , the liquid stream leaving the bioreactor 115 is sent to a separator 140 and a concentrator 145, before the fermentation product(s) is sent for purification. And as in Figure 1 , the retentate and the depleted filtrate may be recycled to bioreactor 135 or used elsewhere in the process 100. But in Figure 2, the gas mixture leaving the reactor 110 and the H2S and NFh are introduced into four separate bioreactors, numbered 115, 116, 117, and 118, that are operating in parallel. The gas streams leaving the bioreactors are then combined and sent to separation device 120, where at least some of the H2S is removed. While Figure 2 shows four gas streams are combined into one and then the combined gas stream entering the separation device 120, it is possible for less than all gas streams to be combined or for each gas stream to enter separation device 120 separately.

Alternatively, two or more gas streams may enter one separation device 120, while other gas streams enter a different separation device 120. In one embodiment, each bioreactor has a separator device 120 dedicated to it, i.e. , only one bioreactor feeds into a separation device. Once the depleted gas stream leaves the separation device 120, the process is essentially the same as in Figure 1.

[00141 ] Figure 3 illustrates an embodiment where an organic substrate enters a reactor 110, where it is converted to a gas mixture comprising COx and H2, where x is 1 and/or 2. While not specified in Figure 3, the reactor 110 may be a single reactor or it may comprise two or more reactors, such as a steam methane reactor (SMR), followed by a water gas shift reactor (WGSR, also referred to as a water gas shift unit). The gas mixture leaving reactor 110 is combined with a nitrogen source and optionally a sulfur source and the resulting gas mixture enters bioreactor 115, which contains an aqueous mixture comprising hydrogenotrophic microorganisms, where it is at least partially converted into a product. The liquid stream comprising the one or more fermentation products leaves the bioreactor 115 and is purified. The gas stream leaving the bioreactor 115 is optionally treated (not shown) before it is recycled to the reactor 110

[00142] Figure 4 diagrams recycle of the liquid stream after product purification. In Figure 4, a gas mixture, comprising COx and H2, where x is 1 and/or 2, is combined with a nitrogen source and optionally a sulfur source, before entering the bioreactor 115. While not shown in Figure 4, if desired, the nitrogen source and sulfur source may be mixed before they are combined with the gas mixture. The gas mixture enters bioreactor 115, which contains an aqueous mixture comprising hydrogenotrophic microorganisms, where it is at least partially converted into one or more fermentation products. The liquid stream leaves the bioreactor 115, and enters a separator 140 where solids and liquids are separated. The fermentation product(s) in the resulting liquid stream is isolated, while the retentate, which includes solids such as the hydrogenotrophic microorganisms, is optionally recycled to the bioreactor 115.

[00143] Figure 5 exemplifies a process where an organic substrate, which can be converted into COx and H2, where x is 1 and/or 2, is fed into reactor 110. While not specified in Figure 5, the reactor 110 may be a single reactor or it may comprise two or more reactors, such as a steam methane reactor (SMR), followed by a water gas shift reactor (WGSR, also referred to as a water gas shift unit). The gas mixture leaving reactor 110 is combined with a nitrogen source and optionally a sulfur source, before entering the bioreactor 115, which contains an aqueous mixture comprising

hydrogenotrophic microorganisms, where it is at least partially converted into one or more fermentation products. While not shown in Figure 5, the nitrogen source and sulfur source may be mixed before they are combined with the gas mixture. The liquid stream leaves the bioreactor 115, and enters a separator 140 where solids and liquids are separated. The fermentation product(s) in the resulting liquid stream is isolated, while the retentate, which includes solids such as the hydrogenotrophic

microorganisms, is optionally recycled to the bioreactor 115. The gas stream leaving bioreactor 115 is then recycled to reactor 110. While not shown in Figure 5, the gas stream may be conditioned by removing or adding various components and/or by changing the pressure of the gas stream.

[00144] In Figure 6, a methane containing gas is fed to an SMR and the material leaving the SMR enters a WGSR, where a gas mixture containing COx and H2, where x is 1 and/or 2 is generated. While the SMR and the WGSR are shown as two distinct reactors in Figure 6, they may be combined into a single reactor (not shown). The gas mixture is combined with a nitrogen source and optionally a sulfur source, before entering the bioreactor 115, which contains an aqueous mixture comprising hydrogenotrophic microorganisms, where it is at least partially converted into one or more fermentation products. While not shown in Figure 6, the nitrogen source and sulfur source may be mixed before they are combined with the gas mixture. The liquid stream leaves the bioreactor 115, and enters a separator 140 where solids and liquids are separated. The one or more fermentation product in the resulting liquid stream is isolated, while the retentate, which includes solids such as the hydrogenotrophic microorganisms, is optionally recycled to the bioreactor 115. The gas stream leaving bioreactor 115 is then recycled to the SMR. While not shown in Figure 6, the gas stream may be combined with the methane containing gas before the gases enter the SMR. Further, the methane containing gas may be treated, by adding or removing components, before it enters the SMR. For example, if the methane containing gas is natural gas, F S may be at least partially removed before the methane containing gas enters the SMR.

[00145] Figure 7 is related to the process illustrated in Figure 6, but in Figure 7, the gas stream leaving the bioreactor 115 is sent to a separation device 125, where at least some H2 is removed, before it is recycled to the SMR. While not specified in Figure 7, the H2 separator may be a pressure swing adsorption unit, a hydrogen membrane or any type of hydrogen separation device. The removed hydrogen may be converted into H2S, burned to generate heat, and/or used in other processes.

[00146] Figure 8 is related to Figure 7, but the gas stream leaving the bioreactor 115 enters a separation device 120, such as an H2S removal device, before it enters separation device 125. The gas stream is recycled to the SMR after leaving the separation device 125. Alternatively, and not shown in Figure 8, separation device 120 may be positioned after separation device 125. In such an embodiment, H2 is removed before the H2S is removed. Additional separation devices, not shown, may be used to further condition the gas stream before it is recycled to the SMR.

[00147] Figure 9 illustrates an embodiment in which the gas mixture exiting the SMR and WGSR enters a H2 separator 125 to remove some of the H2 in the gaseous mixture before the gaseous mixture comprising H2 and COx is mixed with a nitrogen source and an optional sulfur source before entry into the bioreactor 115. The H2 separator may be a pressure swing adsorption unit, a hydrogen membrane or any type of hydrogen separation device. The removed hydrogen may be converted into H2S, burned to generate heat, and/or used in other processes.

[00148] Figure 10 diagrams an embodiment showing purification of the one or more fermentation products. A liquid stream comprising the hydrogenotrophic microorganisms and the one or more fermentation products is removed from the bioreactor 115. The liquid stream enters a separator 140, which comprises a

microfiltration unit and ion exchange chromatography unit. The microfiltration unit separates solids, i.e. , the retentate comprising the hydrogenotrophic microorganisms, from liquids, i.e., filtrate comprising fermentation broth and one or more fermentation products. The retentate may be recycled to the bioreactor 115, it may be used elsewhere in the process, and or it may be discarded. The filtrate, which contains one or more fermentation products, then enters ion exchange chromatography unit in which one or more impurities is removed from the filtrate by binding to the ion exchange resin. The resultant filtrate enters a concentrator 145, which reduces the water content of the filtrate. The concentrated filtrate then enters a crystallizer 150 wherein the crystals of the one or more fermentation products form. The crystals of the one or more

fermentation products are then dried in a drier system 155. The water removed during the concentration process and/or the crystallization process may be stored in a clean water hold tank 160. Although not shown here, the water removed during the

concentration process and/or the crystallization process also may be recycled back to the one or more reactors 110 and/or the bioreactor 115.

[00149] In the processes described in the Figures, various features, such as heat exchangers, nozzles, and baffles may be used, but are not shown.

(II) Systems for Preparing Products by Fermentation

[00150] Also provided herein are systems for preparing one or more fermentation products. Such systems comprise (a) one or more reactors that converts an organic substrate into a gaseous mixture comprising COx and H2, where x is 1 and/or 2; (b) a bioreactor containing non-natural hydrogenotrophic microorganisms that convert the gaseous mixture to at least one fermentation product at a higher level than a parent hydrogenotrophic microorganism, wherein at least one fermentation product is chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; and (c) at least two separation devices that remove at least some of H2S,

CO2, and H2 from a gas stream exciting the bioreactor. In an embodiment, the processes described herein are performed using the systems described herein.

Examples

[00151 ] The following examples illustrate various embodiments or aspects of the present disclosure.

Example 1. Simulated Process - Syngas Production and Fermentation

[00152] The following data were generated using an art accepted modeling program. A combined gas stream that enters a methane stream reformer (SMR) may contain methane (7,577.18 Kg/Hr) in addition to a gas stream containing methane (34,386 Kg/Hr), CO2 (12,304 Kg/Hr) and H2 (984 Kg/Hr). Water (283,860 Kg/Hr) also may be fed into the SMR. A gas stream leaving the SMR may contain H2 (20,926 Kg/Hr), CO2 (126,513 Kg/Hr) and methane (2,098 Kg/Hr) and may be combined with an additional gas stream containing CO2 (2,998), H2S (2,958 Kg/Hr), and NH3 (1 ,804 Kg/Hr). This combined feed enters a bioreactor, where a hydrogenotrophic

microorganism makes methionine, which leaves the bioreactor in an aqueous stream. The methionine may be is isolated from the aqueous stream. A gas mixture leaving the bioreactor may contain methane (35,450 Kg/Hr), H2 (1 ,046 Kg/Hr), CO2 (12,951 Kg/Hr), H2S (29.6 Kg/Hr) and NH3 (180 Kg/Hr) and may be sent to a gas separation unit (membrane or amine stripper). Some of the material leaving the gas separation unit may be the gas stream that is combined with methane (7,577.18 Kg/Hr), above.

Another portion of the material leaving the gas separation unit may contain Nhh (180 Kg/Hr), H2S (30 Kg/Hr), H2 (52 Kg/Hr), methane (1 ,063 Kg/Hr) and CO2 (648 Kg/Hr) and may be sent to an incinerator and/or for recycling.

Example 2. Simulated Process - Generation of Hydrogen Sulfide

[00153] Example 2 is the same as example 1 , except a stream of H2 (174

Kg/Hr) leaving the SMR may be combined with a stream of sulfur (2,784 Kg/Hr), which then enters a sulfur reactor, where some of the material may be sent to an incinerator and/or be converted to H2S, for use in the process.

Example 3. Simulated Process - Fermentation Inputs and Outputs

[00154] The following data were generated using an art accepted modeling program. H₂ (20,927 Kg/Hr), CO2 (129,511 Kg/Hr), methane (2,098Kg/Hr), H2S (2,958 Kg/Hr), and NH3 (1 ,804 Kg/Hr) may enter a bioreactor, where hydrogenotrophic microorganisms make methionine (13,250 Kg/Hr), which leaves the bioreactor as a liquid stream (94,391 Kg/Hr). The gas stream leaving the bioreactor may contain H2 (1 ,046 Kg/Hr), CO2 (12,951 Kg/Hr), methane (35,450 Kg/Hr), H2S (29.6 Kg/Hr), and NHs (180.4 Kg/Hr).

Example 4. Simulated Process - Fermentation

[00155] The following data were generated using an art accepted modeling program. H2 (19,778.97 Kg/Hr), CO2 (123,983.9 Kg/Hr), methane (2,097.995 Kg/Hr), H2S (3,056 Kg/Hr), and NH3 (1 ,693 Kg/Hr) may enter bioreactor, where a

hydrogenotrophic microorganism makes methionine (13,250 Kg/Hr), which may leave the bioreactor as a liquid stream (87,702 Kg/Hr). The gas stream leaving the bioreactor may contain H2 (1 ,046 Kg/Hr), CO2 (12,951 Kg/Hr), methane (35,450 Kg/Hr), H2S (29.6 Kg/Hr), and NHs (180.4 Kg/Hr).

Example 5. Simulated Process - Syngas Production and Fermentation

[00156] The following data were generated using an art accepted modeling program. A gas mixture containing N2, H2, CO, CO2, methane, NH3, and H2O enters the SMR, where CO, CO2 and H2 are formed. The materials leaving the SMR are sent to a water gas shift reactor (WGSR), where the H2 and CO2 content is increased, and the CO and water content is decreased. The contents of the streams entering and exiting the SMR and the WGSR may be as shown in Table 1.

[00157] The syngas leaving the WGSR enters a process condensate knockout drum, where some undesired materials are removed. The syngas is then fed into a bioreactor, along with Nhh (1680 Kg/Hr) and H2S (3186 Kg/Hr). In the bioreactor, a hydrogenotrophic microorganism converts some of the syngas into methionine (88.80 Kg-Mol/Hr). The liquid stream comprising methionine (4899.70 Kg-Mol/Hr) leaves the reactor and the methionine is isolated. A gas stream containing N2, H2, CO, CO2, methane, H2S, NH3, and H2O, leaves the bioreactor and enters an H2S removal system, where the H2S is removed, as shown in Table 2.

[00158] The gas leaving the H2S removal system is initially separated into two streams. The first stream is sulfur, which is used to prepare H2S and/or is discarded. The second stream is split into two streams, the first of which is combined with H2 and used to heat the SMR. The second stream, stream 2A, is sent to an H2 membrane separator. The composition of the second stream may be as shown in Table 3.

[00159] Stream 2A enters a preheater, where it is heated, and then it enters an H2 membrane separator, where three streams are formed. One is H2 that is sent to an H2S reactor, where H2S is prepared. Another is recycled to the SMR, where it is used in the SMR, while the third is combined with the tail gas leaving the H2S removal system, and this combined gas is used to heat the SMR. The contents of these streams may be as shown in Table 4.

the H2S separator, mentioned above.

Example 6. Simulated Process - With CO2 Injection

[00160] The following data were generated using an art accepted modeling program. A gas mixture containing N2, H2, CO, CO2, methane, NH3, and H2O, enters the SMR, where CO, CO2 and H2 are formed. The materials leaving the SMR are sent to a water gas shift reactor (WGSR), where the H2 and CO2 content is increased, and the CO and water content is decreased. Table 5 presents projected contents of the various streams.

[00161 ] The syngas leaving the WGSR enters a process condensate knockout drum, where some undesired materials are removed. The syngas is then fed into a bioreactor, along with NHs (1680 Kg/Hr), H₂S (3186 Kg/Hr) and CO2 (17076 Kg/Hr). In the bioreactor, a hydrogenotrophic microorganism converts some of the gas into methionine (88.81 Kg-Mol/Hr). The liquid stream comprising methionine (4901.16 Kg-Mol/Hr) leaves the reactor and the methionine is isolated. A gas stream containing N2, H2, CO, CO2, methane, H2S, NH3, and H2O, leaves the bioreactor and enters an H2S removal system, where the H2S is removed (see Table 6).

[00162] Two streams leave the H2S removal unit. The first stream is sulfur, which is used to prepare H2S and/or is discarded. The second stream, described immediately above, is split into two streams, the first of which is combined with H2 and used to heat the SMR. The second stream, stream 2A, is condensed and cooled, and then it is split into two streams, 2B and 2C. Stream 2B is recycled to the SMR, where it is used as a reactant. Stream 2C enters an H2 PSA separator. The contents of these streams may be as shown in Table 7.

[00163] In the PSA separator, stream 2C is split into two streams. The first is H2 that is sent to an H2S reactor, where H2S is prepared. The second stream is combined with some of the effluent from the H2S removal system, and used to heat the SMR. The projected contents of these streams are shown in tale 8.

2” stream leaving the H2S separator, mentioned above.

Example 7. Simulated Process - Fermentation

[00164] The following data were generated using an art accepted modeling program. Media, containing water and chemicals that facilitate cell growth, is prepared in a media mix tank. Once formed, the media is pumped out of the mix tank, and then sterilized and de-aerated. The media is then split into multiple streams. One stream is sent to a temperature regulated, first seed fermenter, where it is combined with syngas, Nhh, H2S. Another stream is sent to a temperature regulated, second seed fermenter, where it is combined with syngas, NH3, H2S. A third stream is sent to a temperature regulated, third seed fermenter, where it is combined with syngas, NH3, H2S. Another portion of the media stream is sent to the bioreactor, where it is combined with syngas, NHs, H₂S.

[00165] In the first seed fermenter, the hydrogenotrophic organism begins to grow. Broth, containing the microorganism is then pumped from the first seed fermenter to the temperature regulated, second seed fermenter, where the broth from the first fermenter and the second fermenter mix and additional microorganism growth occurs. The resulting broth is then pumped into the third seed fermenter, where the broths mix and still more microorganism growth occurs. The broth is then pumped out of the third seed fermenter and sent to the bioreactor, where the main preparation of the methionine occurs. De-aerated water can be added to any or all of the aforementioned fermenters and reactors, as needed. Further, each fermenter and reactor may be sterilized by adding a clean in place (CIP) solution that kills the microorganisms. This is necessary if a fermenter and/or reactor becomes contaminated. The fresh media entering the bioreactor may be combined with recycled media, with the different media having the composition shown in Table 9. The composition of recycled media may be as shown in Table 9.

[00166] In the bioreactor, the microorganism converts the syngas, hteS, and Nhta into methionine. Liquid containing the methionine is removed from the bioreactor and sent to a fermenter hold tank. Some of the liquid in the fermenter is pumped to a fermenter kill hold tank, where microorganisms are stored, before they are killed.

Removing older microorganism and replacing them with younger, fresh microorganisms helps to maximize the rate of methionine formation. A second portion of the liquid is returned to the bioreactor. Projected concentrations of methionine and other components in the stream leaving the bioreactor, and in the streams leaving and returning to the bioreactor, may be found in Table 10.

[00167] Recycled broth and recycled cells can be added to the bioreactor. The concentration of the recycled broth and the recycled cells may be as indicated in Table 11 below.

[00168] The methionine containing stream enters a microfiltration system, where three streams are formed. The first stream is a waste water stream, which is sent for treatment. The second stream is sent to an ion exchange system, where it is combined with pure water and HCI. Two streams exit the ion exchange system. One is a waste water stream that is sent for wastewater treatment. The other is sent to a feed evaporator tank, followed by an evaporator (where a water stream is removed and used in other parts of the process), a crystallizer feed tank, a crystallizer, a centrifuge, and then at least one dryer, where 12,710 kg/hr of methionine are isolated. The

compositions of the streams may be as shown in Table 12.

[00169] The water stream leaving the evaporator, above, may be sent to the centrifuge, to the media mix tank, and/or to the reformer (SMR) (Table 13)

[00170] The third stream leaving the microfiltration system is split into two streams. One goes to the fermenters, while the other goes to the kill tanks. The composition of these three streams may be as shown in Table 14.

[00171 ] A gas also leaves the bioreactor and is sent to an amine stripper. The composition of the stream may be as shown in Table 15.

Example 8. Simulated Process - Waste streams

[00172] The following data were generated using an art accepted modeling program. This example is based on Example 7. In this example, the material enters a kill tank where it is treated with a clean in place (CIP) solution, which begins to kill the microorganisms that are present. The stream then enters a decanter, where solids are collected and sent to a solids kill dryer and the dried solids are then discarded. Liquid from the dryer is vented, while liquid from the decanter is mixed with air, under a pressure of 2 bar absolute, thus killing the residual microorganisms. The composition of these streams may be as shown in Table 16.

Example 9. Products produced by continuous fermentation

[00173] Methanococcus maripaludis S2 (TreH O) and a non-natural M.

maripaludis strain (Trel10-Mut333 with a plasmid encoding M. maripaludis LysC(C997A) operably linked to a promoter) were cultured in Balch tubes at 37 °C with agitation, in duplicate. Trel10-333 is described in US Patent Publication 20170130211. Fermentation media in this experiment was McC gassed with 2.CO2 (4:1 ). After 96 hours of fermentation, a sample was obtained from each culture, cells were removed by centrifugation and filtration, and the biological products in the filtrate were evaluated by NMR. Biological products identified by NMR were 2-aminobutyrate, 2- hydroxyisovalerate, 2-oxoglutarate, 2-oxoisocaproate, 3-hydroxyisovalerate, 3-methyl-2- oxovalerate, 4-hydroxybenzoate, ATP, acetate, acetoin, Acetone, alanine, arginine, aspartate, ethanol, glutamate, glutamine, glycerol, glycine, glycolate, hydroxyacetone, isobutyrate, isoleucine, isovalerate, lactate, leucine, methanol, methionine,

phenylalanine, proline, propionate, pyroglutamate, pyruvate, succinate, threonine, tyrosine, and valine. The concentrations of the biological products measured in the samples varied between the two strains.

Example 10. Products produced during a fed-batch fermentation

[00174] A non-natural Methanococcus maripaludis microorganism (TreH O- 333UR pKH32) was cultured under fed-batch fermentative conditions. Trel10-333UR pKH32 is described in US Patent Publication 20170130211. Briefly, fermentation occurred in a single bioreactor (a 3L fermenter with a 1 5L working volume) at 37 °C with agitation. Fermentation media in this experiment was McC plus 2x NFUCI and 2x iron with 1.0 g/L alanine added at EFT 0 and 0.8 g/L alanine added at 39.5, 67.5, and 91.0 EFT. A gas stream consisting of Fte and CO2 (4: 1 ) was fed to the bioreactor at 200ml/min. Sample were taken at different times (EFT 0, 38, 45, 86, 92, and 158), microorganisms removed, and biological products evaluated by NMR. The ODeoo for the samples was 0, 4.0, 3.9, 4.0, 3.8, and 3.0, respectively. Biological products identified by NMR were 2-aminobutyrate, 2-hydroxyisovalerate, 2-oxoglutarate, 2-oxoisocaproate, 3- methyl-2-oxovalerate, 4-hydroxybenzoate, ATP, acetate, acetoin, acetone, alanine, arginine, aspartate, cystine, ethanol, hormate, glutamate, glutamine, glycerol, Glycine, hydroxyacetone, isobutyrate, isoleucine, isovalerate, lactate, leucine, methanol, methionine, phenylalanine, propionate, pyroglutamate, pyruvate, serine, succinate, threonine, tryptophan, tyrosine, and valine. The concentrations of the biological products measured in the samples varied between samples.

Example 11. Products produced during a continuous fermentation

[00175] Two, non-natural Methanococcus maripaludis microorganisms were cultured under continuous fermentative conditions. These strains are Trel10-333UR derivatives that contain additional genetic changes to further increase methionine production. Briefly, fermentation occurred in a single bioreactor (a 3L fermenter with a 1 5L working volume) at 37 °C with agitation. Fermentation media in this experiment was McC plus 2x NFUCI and 2x iron. A gas stream consisting of H2 and CO2 (4:1 ) was fed to the bioreactor at 200m I/m in, and media turnover was 1 2L/day. A liquid stream was continuously withdrawn in order to establish a steady state. After removing the microorganisms, biological products in the liquid stream were evaluated by NMR at 836 and 453 hours of elapsed fermentation time, for strain 1 and strain 2, respectively. The OD6OO for the samples was 3.37 and 3.85, respectively. NMR of media blanks and spiked media blanks served as controls. Biological products identified by NMR were 2- aminobutyrate, 2-hydroxybutyrate, 2-hydroxyvalerate, 3-hydroxybutyrate, 4- hydroxybenzoate, acetate, acetoin, acetone, butyrate, ethanol, formate, glutamate, glycerate, glycerol, isoleucine, isopropanol, lactate, leucine, methanol, methionine, phenylalanine, pyruvate, succinate, tryptophan, and valine. The concentrations of the biological products measured in the samples varied between samples.

[00176] In another experiment, a third non-natural Methanococcus maripaludis microorganism was cultured under continuous fermentative conditions, as generally described above. This strain is Methanococcus maripaludis S2 with a deregulated MMP1359 protein. Fermentation media in this experiment was McC plus 2x NFUCI and 2x iron (sample A and B), or McC plus 2x NFUCI and 2x iron supplemented with 450 mg homocysteine / day (sample C). Biological products in the liquid stream were evaluated by NMR after 521 , 498 and 521 hours of elapsed fermentation time for samples A-C, respectively. The OD6oo for the samples was 2.237, 1.890, and 1.821 , respectively. Biological products identified by NMR were 2-hydroxy-3-methylvalerate, 2- hydroxyisobutyrate, 3-methyl-2-oxovalerate, 4-hydroxybenzoate, 4- hydroxyphenyllactate, acetate, acetoin, acetone, alanine, b-alanine, butyrate, ethanol, formate, fumarate, glutamate, glutamine, glycerol, glycine, isobutyrate, isoleucine, isopropanol, lactate, leucine, lysine, malonate, methanol, methionine, methylamine, phenol, phenylalanine, proline, propionate, pyruvate, succinate, trimethylamine, tryptophan, tyramine, and valine.

Claims

CLAIMS:

What is claimed is:

1. A process for producing one or more product by fermentation, the process

comprising:

(a) feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2;

(b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(c) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2;

(d) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and at least one fermentation product; and

(e) separating the hydrogenotrophic microorganisms from the liquid stream and recycling the hydrogenotrophic microorganisms back to the bioreactor.

2. The process of claim 1 , wherein the one or more reactors contains a catalyst.

3. The process of claim 2, wherein the catalyst is a metal chosen from nickel, cerium, magnesium, rhodium, palladium, platinum, zirconium, lanthanum, samarium, copper, tungsten, rhenium, cobalt, iridium, vanadium, bismuth, aluminum, magnesium, iron, gold, ruthenium, titanium, yttrium, molybdenum, thorium, antimony, gold, strontium, barium, calcium, chromium, silicon, or combinations thereof.

4. The process of any of claims 1 to 3, wherein the one or more reactors is a gasifier, a water gas shift reactor, a steam methane reformer or other reactor that produces H2 and COx, where x is 1 and/or 2.

5. The process of any of claims 1 to 4, wherein the organic substrate is converted to syngas or water-gas shifted syngas.

6. The process of any of claims 1 to 5, wherein the organic substrate is biomass, biogas, natural gas, natural gas liquid, off-gas, oil, carbonaceous material, or

combinations thereof.

7. The process of claim 6, wherein the organic substrate comprises cellulose- containing feedstocks, animal tissue, fish tissue, plant parts, fruits, vegetables, plant processing waste, animal-processing waste, animal manure, animal urine, mammalian manure, mammalian urine, solids isolated from fermentation cultures, bovine manure or urine, poultry manure or urine, equine manure or urine, porcine manure or urine, sawdust, wood shavings, wood chips, wood pulp, bark, slops, pomace, shredded paper, cotton burrs, grain, chaff, seed shells, straw, hay, alfalfa, grass, leaves, sea shells, seed pods, stover, cobs, hulls, pulp, corn shucks, weeds, seaweed, aquatic plants, algae, fungus, or combinations thereof.

8. The process of claim 6, wherein the organic substrate comprises coal, petcoke, resid, or combinations thereof.

9. The process of claim 6, wherein the organic substrate is methane.

10. The process of any of claims 1 to 9, wherein the one or more reactors is maintained at a temperature of from about 200°C to about 900°C.

11. A process for producing one or more product by fermentation, the process comprising:

(a) feeding a gaseous mixture comprising COx and H2, where x is 1 or 2, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(b) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2;

(c) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and fermentation product; and

(d) separating the hydrogenotrophic microorganisms from the liquid stream and recycling the hydrogenotrophic microorganisms back to the bioreactor.

12. The process of any of claims 1 to 11 , wherein the hydrogenotrophic

microorganisms are non-natural hydrogenotrophic microorganisms that produce the fermentation product at a higher level than a parent hydrogenotrophic microorganism.

13. The process of any of claims 1 to 12, wherein the hydrogenotrophic microorganism is chosen from methanogenic archaea, Clostridium, and Knall-gas bacterium.

14. The process of any of claim 13, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium, Methanobrevibacter, Methanocalculus,

Methanocaldococcus, Methanocella, Methanococcus, Methanococcoides,

Methanocorpusculum, Methanoculleus, Methanofollis, Methanogenium,

Methanohalobium, Methanohalophilus, Methanolacinia, Methanolobus,

Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter, Methanothermococcus, Methanothermus, and Methanotorris.

15. The process of claim 14, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae,

Methanobacterium formicicum, Methanobacterium ivanovii, Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum,

Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus,

Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocella arvoryzae, Methanocella conradii,

Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii, Methanothermus sociabilis,

Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus, Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila, Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus

thermolithotrophicus, Methanopyrus kandleri, Methanothermobacter

thermoautotroiphicus, Methanocaldococcus fervens, Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, and

Methanocaldococcus vulcanius.

18. The process of claim 13, wherein the hydrogenotrophic microorganism is chosen from Methanococcus, and Methanosarcina.

17. The process of claim 16, wherein the hydrogenotrophic microorganism is a Methanococcus species.

18. The process of claim 16, wherein the hydrogenotrophic microorganism is a Methanosarcina species.

19. The process of any one of claims 1 to 18, wherein the process is continuous, batch, or fed batch.

20. The process of claim 19, wherein the process is continuous.

21. The process of any one of claims 1 to 20, wherein the bioreactor is a stirred tank, packed bed, one liquid phase, two liquid phase, hollow fiber membrane, bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), air lift, loop, or fluidized bed bioreactor.

22. The process of any one of claims 1 to 21 , wherein the concentration of the hydrogenotrophic microorganism in the bioreactor is about 1 g/L to about 100 g/L.

23. The process of any one of claims 1 to 22, wherein the temperature inside the bioreactor is about 25°C to about 85°C and the pH is from about 6.5 to 7.5.

24. The process of any one of claims 1 to 23, wherein the pressure inside the bioreactor is greater than about 1 bar absolute.

25. The process any one of claims 1 to 24, wherein the amount of CO in the gaseous mixture is no more than about 35%.

26. The process of any one of claims 1 to 25, wherein the amount of CO in the gaseous mixture is no more than about 8%.

27. The process of any one of claims 1 to 26, wherein the ratio of CO2 to H2 in the gaseous mixture ranges from about 1 :50 to about 10:1 , respectively.

28. The process of any one of claims 1 to 27, wherein the nitrogen source comprises ammonia or an ammonia derivative.

29. The process of any one of claims 1 to 28, wherein the sulfur source is present and comprises a sulfide or a sulfide derivative.

30. The process of any one of claims 1 to 29, wherein the gas mixture, sulfur source and the nitrogen source are not mixed together before entering the bioreactor.

31. The process of any one of claims 1 to 29, wherein the nitrogen source and the sulfur source, and optionally the gaseous mixture, are mixed together before entering the bioreactor.

32. The process of any one of claims 1 to 31 , wherein the gas stream removed from the bioreactor comprises a combination of at least two of H2, H2S, Nhh, CO, CO2 and methane.

33. The process of any one of claims 1 to 32, wherein the gas stream is recycled back to one or both of the one or more reactors or the bioreactor.

34. The process of claim 33, wherein after the gas stream leaves the bioreactor it enters a separation device that removes at least some of the H2S, CO2 or both from the gas stream.

35. The process of claim 34, wherein the gas stream is recycled back to one or both of the one or more reactors or bioreactor after leaving the separation device.

36. The process of claim 34 or 35, wherein the separation device contains a catalyst.

37. The process of claim 33, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

38. The process of claim 33, wherein after the gas stream leaves the bioreactor it enters at least two separation devices wherein the separation devices remove at least some of the H2S, CO2 and H2 from the gas stream before the gas stream is recycled back to one or both of the one or more reactors or bioreactor.

39. The process of claim 38, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

40. The process of any of claims 37 to 39, wherein the H2 separation device comprises a pressure swing adsorption unit or a hydrogen membrane.

41. The process of any of claims 37 to 39, wherein the H2 separation device is a hydrogen membrane.

42. The process of any of claims 1 to 41 , wherein the gas stream is pressurized before being recycled back to one or both of the one or more reactors or bioreactor.

43. The process of any of claims 1 to 42, further comprising separating the liquid stream to produce a retentate comprising a concentrated amount of the hydrogenotrophic microorganisms and a filtrate comprising a reduced amount of the hydrogenotrophic microorganisms and one or more fermentation product in fermentation broth.

44. The process of claim 43, wherein from about 1 % to 3% by weight of the retentate is removed as purge prior to recycling the retentate back to the bioreactor.

45. The process of claim 43 or 44, wherein the liquid stream is separated using microfiltration.

46. The process of any of claims 43 to 45, wherein the one or more fermentation product is purified from the filtrate to form a fermentation product depleted filtrate fraction.

47. The process of claim 46, wherein an aqueous composition is removed from the depleted filtrate fraction and the aqueous composition is recycled back to one or both of the one or more reactors or bioreactor.

48. The process of 46, wherein the one or more fermentation product is purified via a process chosen from extraction, drying, chromatography, crystallization, dialysis, solvent extraction, and a combination thereof.

49. A system for preparing one or more product by fermentation, the system

comprising:

(a) one or more reactors that converts an organic substrate into a gaseous mixture comprising COx and H2, where x is 1 and/or 2;

(b) a bioreactor containing non-natural hydrogenotrophic microorganisms that convert the gaseous mixture to at least one fermentation product at a higher level than a parent hydrogenotrophic microorganism, wherein at least one fermentation product is chosen from an amino acid, a TCA cycle product, an alcohol, an alcohol precursor, a short chain carboxylic acid, a fatty acid, a fatty acid conjugate, phenol, and a phenol derivative; and

(c) at least two separation devices that remove at least some of H2S, CO2, and H2 from a gas stream exiting the bioreactor.

50. The process of any one of claims 1 to 48, or system of claim 49, wherein the fermentation product is an amino acid.

51. The process or system of claim 50, wherein the amino acid is at least one chosen from lysine, threonine, glycine and methionine.

52. The process of any one of claims 1 to 48, or system of claim 49, wherein the fermentation product is an alcohol, aldehyde or ketone.

53. The process or a system of claim 52, wherein the alcohol, aldehyde or ketone is at least one chosen from glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

54. The process of any one of claims 1 to 48, or system of claim 49, wherein the fermentation product is a carboxylic acid.

55. The process or system of claim 54, wherein the carboxylic acid is at least one chosen from acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, or succinate.

56. The process of any one of claims 1 to 48, or system of claim 49, wherein the fermentation product is a hydroxy acid or a keto acid.

57. The process or system of claim 56, wherein the hydroxy or keto acid is at least one chosen from 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, or pyruvate.

58. A process for producing one or more product by fermentation, the process comprising:

(a) feeding an organic substrate into one or more reactor under conditions to generate a gaseous mixture comprising COx and hte, where x is 1 or 2;

(b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid; (c) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2; and

(d) recycling at least a portion of the gas stream back to the one or more reactors or the bioreactor.

59. The process of claim 58, wherein the one or more reactors contains a catalyst.

60. The process of claim 59, wherein the catalyst is a metal chosen from nickel, cerium, magnesium, rhodium, palladium, platinum, zirconium, lanthanum, samarium, copper, tungsten, rhenium, cobalt, iridium, vanadium, bismuth, aluminum, magnesium, iron, gold, ruthenium, titanium, yttrium, molybdenum, thorium, antimony, gold, strontium, barium, calcium, chromium, silicon, or combinations of two or more thereof

61. The process of any of claims 57 to 60, wherein the one or more reactors is a gasifier, water gas shift reactor, a steam methane reformer or other reactor that produces H2 and COx, where x is 1 and/or 2.

62. The process of any of claims 57 to 61 , wherein the organic substrate is converted to syngas or water-gas shifted syngas.

63. The process of any of claims 57 to 62, wherein the organic substrate is biomass, biogas, natural gas, natural gas liquid, off-gas, oil, carbonaceous material, or

combinations thereof.

64. The process of claim 63, wherein the organic comprises cellulose-containing feedstocks, animal tissue, fish tissue, plant parts, fruits, vegetables, plant-processing waste, animal-processing waste, animal manure, animal urine, mammalian manure, mammalian urine, solids isolated from fermentation cultures, bovine manure or urine, poultry manure or urine, equine manure or urine, porcine manure or urine, sawdust, wood shavings, wood chips, wood pulp, bark, slops, pomace, shredded paper, cotton burrs, grain, chaff, seed shells, straw, hay, alfalfa, grass, leaves, sea shells, seed pods, stover, cobs, hulls, pulp, corn shucks, weeds, seaweed, aquatic plants, algae, fungus, or combinations thereof.

65. The process of claim 63, wherein the organic substrate comprises coal, petcoke, resid, or combinations thereof.

66. The process of claim 63, wherein the organic substrate is methane.

67. The process of any of claims 58 to 66, wherein the one or more reactors is maintained at a temperature from about 200°C to about 900°C.

68. A process for producing one or more product by fermentation, the process comprising:

(a) feeding a gaseous mixture comprising COx and H2, where x is 1 or 2, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(b) removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2; and

(c) recycling at least a portion of the gas stream back to the bioreactor.

69. The process of any of claims 58 to 68, wherein the hydrogenotrophic

microorganisms are non-natural hydrogenotrophic microorganisms that produce one or more fermentation product at a higher level than a parent hydrogenotrophic

microorganism.

70. The process of any of claims 58 to 69, wherein the hydrogenotrophic microorganism is chosen from methanogenic archaea, Clostridium, and Knall-gas bacterium.

71. The process of any of claims 58 to 70, wherein the hydrogenotrophic

microorganism is chosen from Methanobacterium, Methanobrevibacter,

Methanocalculus, Methanocaldococcus, Methanocella, Methanococcus,

Methanococcoides, Methanocorpusculum, Methanoculleus, Methanofollis,

Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,

Methanolobus, Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter,

Methanothermococcus, Methanothermus, or Methanotorris.

72. The process of any of claims 58 to 71 , wherein the hydrogenotrophic

microorganism is chosen from Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae, Methanobacterium formicicum, Methanobacterium ivanovii,

Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum, Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus, Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocella arvoryzae, Methanocella conradii,

Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii, Methanothermus sociabilis,

Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus, Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila,

Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus

thermolithotrophicus, Methanopyrus kandleri, Methanothermobacter

thermoautotroiphicus, Methanocaldococcus fervens, Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, or

Methanocaldococcus vulcanius.

73. The process of any of claims 58 to 72, wherein the hydrogenotrophic

microorganism is chosen from Methanococcus or Methanosarcina.

74. The process of claim 73, wherein the hydrogenotrophic microorganism is a

Methanococcus species.

75. The process of claim 73, wherein the hydrogenotrophic microorganism is a

Methanosarcina species.

76. The process of any one of claims 58 to 75, wherein the process is continuous, batch, or fed batch.

77. The process of any one of claims 58 to 76, wherein the process is continuous.

78. The process of any one of claims 58 to 77, wherein the bioreactor is a stirred tank, packed bed, one liquid phase, two liquid phases, hollow fiber membrane, bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), air lift, loop, or fluidized bed bioreactor.

79. The process of any one of claims 58 to 78, wherein the concentration of the hydrogenotrophic microorganism in the bioreactor is about 1 g/L to about 100 g/L.

80. The process of any one of claims 58 to 79, wherein the temperature inside the bioreactor is about 25°C to about 85°C and the pH is from about 6.5 to 7.5.

81. The process of any one of claims 58 to 80, wherein the pressure inside the bioreactor is greater than about 1 bar absolute.

82. The process any one of claims 58 to 81 , wherein the amount of CO in the gaseous mixture is no more than about 35%.

83. The process of any one of claims 58 to 82, wherein the amount of CO in the gaseous mixture is no more than about 8%.

84. The process of any one of claims 58 to 83, wherein the ratio of CO2 to H2 in the gaseous mixture ranges from about 1 : 50 to about 10:1 , respectively.

85. The process of any one of claims 58 to 84, wherein the nitrogen source comprises ammonia or an ammonia derivative.

86. The process of any one of claims 58 to 85, wherein the sulfur source is present and comprises a sulfide or a sulfide derivative.

87. The process of any one of claims 58 to 86, wherein the gaseous mixture, sulfur source and the nitrogen source are not mixed together before entering the bioreactor.

88. The process of any one of claims 58 to 86, wherein the nitrogen source and the sulfur source, and optionally the gaseous mixture, are mixed together before entering the bioreactor.

89. The process of any one of claims 58 to 88, wherein the gas stream removed from the bioreactor comprises a combination of at least two of H2, H2S, NH3, CO, CO2 and methane.

90. The process of claim 89, wherein after the gas stream leaves the bioreactor it enters a separation device that removes at least some of the H2S, CO2 or both from the gas stream.

91. The process of claim 90, wherein the gas stream is recycled back to one or both of the one or more reactor or bioreactor after leaving the separation device.

92. The process of claim 90 or 91 , wherein the separation device contains a catalyst.

93. The process of claim 89, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

94. The process of claim 89, wherein after the gas stream leaves the bioreactor it enters at least two separation devices wherein the separation devices remove at least some of the H2S, CO2 and H2 from the gas stream before the gas stream is recycled back to one or both of the one or more reactors or bioreactor.

95. The process of claims 94, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

96. The process of any one of claims 93 to 95, wherein the H2 separation device comprises a pressure swing adsorption unit or a hydrogen membrane.

97. The process of any one of claims 93 to 95, wherein the H2 separation device is a hydrogen membrane.

98. The process of any of claims 58 to 97, wherein the gas stream is pressurized before being recycled back to one or both of the reactor or bioreactor.

99. The process of any of claims 58 to 98, wherein the gas stream recycled back to the reactor or bioreactor comprises methane and COx where x is 1 or 2.

100. The process of any of claims 58 to 99, wherein the one or more fermentation products are purified from the fermentation broth via a process chosen from

microfiltration, ion exchange chromatography, evaporation, crystallization, drying, dialysis, solvent extraction, or a combination thereof.

101. The process of any one of claims 58 to 100, wherein the fermentation product is an amino acid.

102. The process of claim 101 , wherein the amino acid is at least one chosen from lysine, threonine, glycine or methionine.

103. The process of any one of claims 58 to 100, wherein the fermentation product is an alcohol, aldehyde or ketone.

104. The process or a system of claim 103, wherein the alcohol, aldehyde or ketone is at least one chosen from glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

105. The process of any one of claims 58 to 100, wherein the fermentation product is a carboxylic acid.

106. The process or system of claim 105, wherein the carboxylic acid is at least one chosen from acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, or succinate.

107. The process of any one of claims 58 to 100, wherein the fermentation product is a hydroxy acid or a keto acid.

108. The process or system of claim 107, wherein the hydroxy or keto acid is at least one chosen from 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, or pyruvate.108. A process for producing one or more product by fermentation, the process comprising:

(a) feeding an organic substrate into one or more reactor under conditions to generate a gaseous mixture comprising COx and hte, where x is 1 or 2;

(b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(c) removing a liquid stream from the bioreactor;

(d) separating hydrogenotrophic microorganisms from the liquid stream; and

(e) recycling the hydrogenotrophic microorganisms to the bioreactor.

109. The process of claim 108, wherein the one or more reactors contains a catalyst.

110. The process of claim 109, wherein the catalyst is a metal chosen from nickel, cerium, magnesium, rhodium, palladium, platinum, zirconium, lanthanum, samarium, copper, tungsten, rhenium, cobalt, iridium, vanadium, bismuth, aluminum, magnesium, iron, gold, ruthenium, titanium, yttrium, molybdenum, thorium, antimony, gold, strontium, barium, calcium, chromium, silicon, or combinations of two or more thereof

111. The process of any of claims 108 to 110, wherein the one or more reactors is a gasifier, a water gas shift reactor, a steam methane reformer or other reactor that produces H2 and COx, where x is 1 and/or 2.

112. The process of any of claims 108 to 111 , wherein the organic substrate is converted to syngas or water-gas shifted syngas.

113. The process of any of claims 108 to 112, wherein the organic substrate is biomass, biogas, natural gas, natural gas liquid, off-gas, oil, carbonaceous material, or combinations thereof.

114. The process of claim 113, wherein the organic substrate comprises cellulose- containing feedstocks, animal tissue, fish tissue, plant parts, fruits, vegetables, plant processing waste, animal-processing waste, animal manure, animal urine, mammalian manure, mammalian urine, solids isolated from fermentation cultures, bovine manure or urine, poultry manure or urine, equine manure or urine, porcine manure or urine, sawdust, wood shavings, wood chips, wood pulp, bark, slops, pomace, shredded paper, cotton burrs, grain, chaff, seed shells, straw, hay, alfalfa, grass, leaves, sea shells, seed pods, stover, cobs, hulls, pulp, corn shucks, weeds, seaweed, aquatic plants, algae, fungus, or combinations thereof.

115. The process of claim 113, wherein the organic substrate comprises coal, petcoke, resid, or combinations thereof.

116. The process of claim 113, wherein the organic substrate is methane.

117. The process of any of claims 108 to 116, wherein the one or more reactors is maintained at a temperature from about 200°C to about 900°C.

118. A process for producing one or more product by fermentation, the process comprising:

(a) feeding a gaseous mixture comprising COx and H2, where x is 1 or 2, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms in a fermentation broth under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(b) removing a liquid stream from the bioreactor; (c) separating hydrogenotrophic microorganisms from the liquid stream; and

(d) recycling the hydrogenotrophic microorganisms to the bioreactor.

119. The process of any of claims 108 to 118, wherein the hydrogenotrophic microorganisms are non-natural hydrogenotrophic microorganisms that produce one or more fermentation product at a higher level than a parent hydrogenotrophic

microorganism.

120. The process of any of claims 108 to 119, wherein the hydrogenotrophic microorganism is chosen from methanogenic archaea, Clostridium, or Knall-gas bacterium.

121. The process of any of claims 108 to 120, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium, Methanobrevibacter,

Methanocalculus, Methanocaldococcus, Methanocella, Methanococcus,

Methanococcoides, Methanocorpusculum, Methanoculleus, Methanofollis,

Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,

Methanolobus, Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter,

Methanothermococcus, Methanothermus, or Methanotorris.

122. The process of any of claims 108 to 121 , wherein the hydrogenotrophic microorganism is chosen from Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae, Methanobacterium formicicum, Methanobacterium ivanovii,

Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum, Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus, Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocella arvoryzae, Methanocella conradii, Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii, Methanothermus sociabilis,

Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus, Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila, Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus

thermolithotrophicus, Methanopyrus kandleri, Methanothermobacter

thermoautotroiphicus, Methanocaldococcus fervens, Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, or

Methanocaldococcus vulcanius.

123. The process of any of claims 108 to 122, wherein the hydrogenotrophic microorganism is chosen from Methanococcus or Methanosarcina.

124. The process of claim 123, wherein the hydrogenotrophic microorganism is a Methanococcus species.

125. The process of claim 123, wherein the hydrogenotrophic microorganism is a Methanosarcina species.

126. The process of any one of claims 108 to 125, wherein the process is continuous, batch, or fed batch.

127. The process of any one of claims 108 to 126, wherein the process is continuous.

128. The process of any one of claims 108 to 127, wherein the bioreactor is a stirred tank, packed bed, one liquid phase, two liquid phase, hollow fiber membrane, bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), air lift, loop, or fluidized bed bioreactor.

129. The process of any one of claims 108 to 128, wherein the concentration of the hydrogenotrophic microorganism in the bioreactor is about 1 g/L to about 100 g/L.

130. The process of any one of claims 108 to 129, wherein the temperature inside the bioreactor is about 25°C to about 85°C and the pH is from about 6.5 to 7.5.

131. The process of any one of claims 108 to 130, wherein the pressure inside the bioreactor is greater than about 1 bar absolute.

132. The process any one of claims 108 to 131 , wherein the amount of CO in the gaseous mixture is no more than about 35%.

133. The process of any one of claims 108 to 132, wherein the amount of CO in the gaseous mixture is no more than about 8%.

134. The process of any one of claims 108 to 133, wherein the ratio of CO2 to H2 in the gaseous mixture ranges from about 1 :50 to about 10:1 , respectively.

135. The process of any one of claims 108 to 134, wherein the nitrogen source comprises ammonia or an ammonia derivative.

136. The process of any one of claims 108 to 135, wherein the sulfur source is present and comprises a sulfide or a sulfide derivative.

137. The process of any one of claims 108 to 136, wherein the gaseous mixture, sulfur source and the nitrogen source are not mixed together before entering the bioreactor.

138. The process of any one of claims 108 to 136, wherein the nitrogen source and the sulfur source, and optionally the gaseous mixture, are mixed together before entering the bioreactor.

139. The process of any one of claims 108 to 138, wherein a gas stream is removed from the bioreactor comprising a combination of at least two of H2, H2S, NH3, CO, CO2 and methane.

140. The process of any one of claims 108 to 139, wherein the gas stream is recycled back to one or both of the one or more reactors or bioreactor.

141. The process of claim 139, wherein after the gas stream leaves the bioreactor it enters a separation device that removes at least some of the H2S, CO2 or both from the gas stream.

142. The process of claim 141 , wherein the gas stream is recycled back to one or both of the one or more reactors or bioreactor after leaving the first separation device.

143. The process of claim 141 or 142, wherein the separation device contains a catalyst.

144. The process of claim 143, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

145. The process of claim 143, wherein after the gas stream leaves the bioreactor it enters at least two separation devices wherein the separation devices remove at least some of the H2S, CO2 and H2 from the gas stream before the gas stream is recycled back to one or both of the one or more reactors or bioreactor.

146. The process of claim 145, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

147. The process of any of claims 144 to 146, wherein the H2 separation device comprises a pressure swing adsorption unit or a hydrogen membrane.

148. The process of any of claims 144 to 146, wherein the H2 separation device is a hydrogen membrane.

149. The process of any of claims 108 to 148, wherein the gas stream is pressurized before being recycled back to one or both of the one or more reactors or bioreactor.

150. The process of any of claims 108 to 149, further comprising separating the liquid stream to produce a retentate comprising a concentrated amount of the

hydrogenotrophic microorganisms and a filtrate comprising a reduced amount of the hydrogenotrophic microorganisms and one or more fermentation product in

fermentation broth.

151 . The process of claim 150, wherein from about 1 % to 3% by weight of the retentate is removed as purge prior to recycling the retentate back to the bioreactor.

152. The process of claim 150 or 151 , wherein the liquid stream is separated using microfiltration.

153. The process of any of claims 151 to 152, wherein the one or more fermentation product is purified from the filtrate to form a fermentation product depleted filtrate fraction.

154. The process of claim 153, wherein an aqueous composition is removed from the depleted filtrate fraction and the aqueous composition is recycled back to one or both of the one or more reactors or bioreactor.

155. The process of 153, wherein the one or more fermentation products are purified via a process chosen from microfiltration, ion exchange chromatography, evaporation, crystallization, drying, dialysis, solvent extraction, or a combination thereof.

156. The process of any one of claims 108 to 155, wherein the fermentation product is an amino acid.

157. The process or a system of claim 156, wherein the amino acid is at least one chosen from lysine, threonine, glycine or methionine.

158. The process of any one of claims 108 to 155, wherein the fermentation product is an alcohol, aldehyde or ketone.

159. The process or a system of claim 158, wherein the alcohol, aldehyde or ketone is at least one chosen from glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

160. The process of any one of claims 108 to 155, wherein the fermentation product is a carboxylic acid.

161. The process or system of claim 160, wherein the carboxylic acid is at least one chosen from acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, or succinate.

162. The process of any one of claims 108 to 155, wherein the fermentation product is a hydroxy acid or a keto acid.

163. The process or system of claim 162, wherein the hydroxy or keto acid is at least one chosen from 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, or pyruvate.

Fermentation product purification claims:

164. A process for purifying one or more fermentation products from a fermentation liquid stream, the process comprising:

(a) culturing hydrogenotrophic microorganisms in a bioreactor under fermentative conditions to produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(b) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and one or more fermentation product; and

(c) purifying the one or more fermentation product from the liquid stream.

165. The process of claim 164, further comprising separating the hydrogenotrophic microorganisms from the liquid stream and recycling the hydrogenotrophic

microorganisms back to the bioreactor.

166. The process of claim 164 or 165, wherein the one or more fermentation product are purified via a process chosen from microfiltration, ion exchange chromatography, evaporation, crystallization, drying, dialysis, solvent extraction, or a combination thereof.

167. The process of any of claim 164 to 166, wherein step (b) further comprises filtering the liquid stream to produce a solid fraction comprising a concentrated amount of the hydrogenotrophic microorganisms and a liquid fraction comprising a reduced amount of the hydrogenotrophic microorganisms one or more fermentation product in fermentation broth.

168. The process of claim 167, wherein the liquid stream is filtered using microfiltration.

169. The process of claim 167 or 168, wherein the liquid fraction is subjected to ion exchange chromatography in a manner such that at least one impurity is retained on the ion exchange media thereby separating the at least one impurity from the one or more fermentation products in the liquid fraction, or wherein one or more fermentation product is retained on the ion exchange media thereby separating the one or more fermentation product from other components in the liquid fraction.

170. The process of any of claims 167 to 169, wherein the one or more fermentation product are purified from the liquid fraction to form a fermentation product depleted filtrate fraction.

171. The process of any of claim 164 to 170, wherein the liquid stream or liquid fraction is subjected to evaporation to form a fermentation product concentrated fraction.

172. The process of claim 171 , wherein the evaporation is conducted at a temperature of about 120° C.

173. The process of claim 172, wherein one or more fermentation product are concentrated to about 14% by weight of the liquid stream or liquid fraction.

174. The process of any of claims 171 to 173, wherein the one or more fermentation product concentrated fraction is subjected to a crystallization process.

175. The process of claim 174, wherein the crystallization process is conducted via forced circulation crystallizers.

176. The process of claim 174 or 175, wherein the crystallization procedure is conducted under vacuum.

177. The process of any of claims 174 to 76, wherein after the crystallization procedure the solution is cooled to a temperature of about 25° to about 30° C resulting in formation of crystals of the one or more fermentation product.

178. The process of claim 177, wherein the crystals of the one or more fermentation product are isolated from the solution via centrifugation.

179. The process of claim 178, wherein the crystals of the one or more fermentation product have a moisture content of less than about 20%.

180. The process of claim 178 or 179, wherein the crystals of the one or more fermentation product are dried.

181. The process of claim 180, wherein the crystals of the one or more fermentation product are dried via a fluidized dryer system.

182. The process of claim 180 or 181 , wherein the crystals of the one or more fermentation product have a moisture content of less than about 1 % after the drying procedure.

183. The process of any of claims 180 to 182, wherein the temperature during the drying procedure does not exceed about 60° C.

184. The process of any of claim 164 to 183, wherein at least a portion of the water removed during any process conducted to purify the one or more fermentation product is recycled back to the bioreactor.

185. The process of any of claim 164 to 184, wherein the hydrogenotrophic

microorganisms are non-natural hydrogenotrophic microorganisms that produce the one or more fermentation product at a higher level than a parent hydrogenotrophic microorganism.

186. The process of any of claim 164 to 185, wherein the hydrogenotrophic microorganism is chosen from methanogenic archaea, Clostridium, or Knall-gas bacterium.

187. The process of any of claim 164 to 186, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium, Methanobrevibacter,

Methanocalculus, Methanocaldococcus, Methanocella, Methanococcus,

Methanococcoides, Methanocorpusculum, Methanoculleus, Methanofollis,

Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,

Methanolobus, Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter,

Methanothermococcus, Methanothermus, or Methanotorris.

188. The process of any of claim 164 to 187, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae, Methanobacterium formicicum, Methanobacterium ivanovii,

Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum, Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus, Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocella arvoryzae, Methanocella conradii,

Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii, Methanothermus sociabilis,

Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus, Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila,

Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus

thermolithotrophicus, Methanopyrus kandleri, Methanothermobacter

thermoautotroiphicus, Methanocaldococcus fervens, Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, or

Methanocaldococcus vulcanius.

189. The process of any of claim 164 to 188, wherein the hydrogenotrophic

microorganism is chosen from Methanococcus or Methanosarcina.

190. The process of claim 189, wherein the hydrogenotrophic microorganism is a Methanococcus species.

191. The process of claim 189, wherein the hydrogenotrophic microorganism is a Methanosarcina species.

192. The process of any one of claim 164 to 191 , wherein the process is continuous, batch, or fed batch.

193. The process of any one of claim 164 to 192, wherein the process is continuous.

194. The process of any one of claim 164 to 193, wherein the fermentation product is an amino acid.

195. The process or system of claim 194, wherein the amino acid is at least one chosen from lysine, threonine, glycine and methionine.

196. The process of any one of claim 164 to 193, wherein the fermentation product is an alcohol, aldehyde or ketone.

197. The process or a system of claim 196, wherein the alcohol, aldehyde or ketone is at least one chosen from glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

198. The process of any one of claim 164 to 193, wherein the fermentation product is a carboxylic acid.

199. The process or system of claim 198, wherein the carboxylic acid is at least one chosen from acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, or succinate.

200. The process of any one of claim 164 to 193, wherein the fermentation product is a hydroxy acid or a keto acid.

201. The process or system of claim 200, wherein the hydroxy or keto acid is at least one chosen from 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, or pyruvate.

Fermentation process with water recycle claims:

201. A process for producing one or more products by fermentation, the process comprising:

(a) feeding an organic substrate into one or more reactors under conditions to generate a gaseous mixture comprising COx and H2, where x is 1 or 2;

(b) feeding the gaseous mixture, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(c) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and at least one fermentation product; and

(d) purifying the at least one fermentation product from the liquid stream, wherein the purification requires at least one procedure where water is removed from the liquid stream; and

(e) recycling the water back to the one or more reactors of step (a), and/or to the bioreactor of step (b), and/or to a clean water hold tank.

202. The process of claim 201 , wherein the one or more reactors contains a catalyst.

203. The process of claim 202, wherein the catalyst is a metal chosen from nickel, cerium, magnesium, rhodium, palladium, platinum, zirconium, lanthanum, samarium, copper, tungsten, rhenium, cobalt, iridium, vanadium, bismuth, aluminum, magnesium, iron, gold, ruthenium, titanium, yttrium, molybdenum, thorium, antimony, gold, strontium, barium, calcium, chromium, silicon, or combinations thereof.

204. The process of any of claims 201 to 203, wherein the one or more reactors is a gasifier, a water gas shift reactor, a steam methane reformer or other reactor that produces H2 and COx, where x is 1 and/or 2.

205. The process of any of claims 201 to 204, wherein the organic substrate is converted to syngas or water-gas shifted syngas.

206. The process of any of claims 201 to 205, wherein the organic substrate is biomass, biogas, natural gas, natural gas liquid, off-gas, oil, carbonaceous material, or combinations thereof.

207. The process of claim 206, wherein the organic substrate comprises cellulose- containing feedstocks, animal tissue, fish tissue, plant parts, fruits, vegetables, plant processing waste, animal-processing waste, animal manure, animal urine, mammalian manure, mammalian urine, solids isolated from fermentation cultures, bovine manure or urine, poultry manure or urine, equine manure or urine, porcine manure or urine, sawdust, wood shavings, wood chips, wood pulp, bark, slops, pomace, shredded paper, cotton burrs, grain, chaff, seed shells, straw, hay, alfalfa, grass, leaves, sea shells, seed pods, stover, cobs, hulls, pulp, corn shucks, weeds, seaweed, aquatic plants, algae, fungus, or combinations thereof.

208. The process of claim 206, wherein the organic substrate comprises coal, petcoke, resid, or combinations thereof.

209. The process of any claim 206, wherein the organic substrate is methane.

210. The process of any of claims 201 to 209, wherein the one or more reactors is maintained at a temperature of from about 200°C to about 900°C.

211. A process for producing one or more product by fermentation, the process comprising:

(a) feeding a gaseous mixture comprising COx and H2, where x is 1 or 2, a nitrogen source, and optionally a sulfur source to a bioreactor that contains hydrogenotrophic microorganisms under conditions such that the hydrogenotrophic microorganisms produce at least one fermentation product chosen from an amino acid, an alcohol, aldehyde or ketone, a carboxylic acid, or a hydroxyl or keto acid;

(b) removing a liquid stream from the bioreactor comprising fermentation broth, hydrogenotrophic microorganisms, and at least one fermentation product; and

(c) purifying the at least one fermentation product from the liquid stream, wherein the purification requires at least one procedure where water is removed from the liquid stream; and

(d) recycling the water back to the bioreactor of step (b), and/or to a clean water hold tank.

212. The process of any of claims 201 to 211 , wherein the at least one procedure where water is removed comprises microfiltration, ion exchange chromatography, evaporation, crystallization, dialysis, solvent extraction, or combinations thereof.

213. The process of any of the claims 201 to 212, wherein the water is de-gassed after removal.

214. The process of any of claims 201 to 213, wherein the hydrogenotrophic microorganisms are non-natural hydrogenotrophic microorganisms that produce the fermentation product at a higher level than a parent hydrogenotrophic microorganism.

215. The process of any of claims 201 to 214, wherein the hydrogenotrophic microorganism is chosen from methanogenic archaea, Clostridium, or Knall-gas bacterium.

216. The process of any of claims 201 to 215, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium, Methanobrevibacter,

Methanocalculus, Methanocaldococcus, Methanocella, Methanococcus,

Methanococcoides, Methanocorpusculum, Methanoculleus, Methanofollis,

Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,

Methanolobus, Methanomethylovorans, Methanomicrobium, Methanomicrococcus, Methanoplanus, Methanopyrus, Methanoregula, Methanosaeta, Methanosalsum, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter,

Methanothermococcus, Methanothermus, or Methanotorris.

217. The process of any of claims 201 to 216, wherein the hydrogenotrophic microorganism is chosen from Methanobacterium alcaliphilum, Methanobacterium bryantii, Methanobacterium congolense, Methanobacterium defluvii, Methanobacterium espanolae, Methanobacterium formicicum, Methanobacterium ivanovii,

Methanobacterium palustre, Methanobacterium thermaggregans, Methanobacterium uliginosum, Methanobrevibacter acididurans, Methanobrevibacter arboriphilicus, Methanobrevibacter gottschalkii, Methanobrevibacter olleyae, Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanobrevibacter woesei,

Methanobrevibacter wolinii, Methanocella arvoryzae, Methanocella conradii,

Methanocella paludicola, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicum, Methanothermobacter thermoflexus, Methanothermobacter thermophilus, Methanothermobacter wolfeii, Methanothermus sociabilis,

Methanocorpusculum bavaricum, Methanocorpusculum parvum, Methanoculleus chikuoensis, Methanoculleus submarinus, Methanogenium frigidum, Methanogenium liminatans, Methanogenium marinum, Methanomicrococcus blatticola, Methanoplanus endosymbiosus, Methanoplanus limicola, Methanoplanus petrolearius, Methanopyrus kandleri, Methanoregula boonei, Methanosaeta concilii, Methanosaeta harundinacea, Methanosaeta pelagica, Methanosaeta thermophila, Methanosarcina acetivorans, Methanosarcina barkeri, Methanosarcina mazei, Methanosarcina thermophila, Methanomicrobium mobile, Methanococcus aeolicus, Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltae, Methanothermococcus

thermolithotrophicus, Methanopyrus kandleri, Methanothermobacter

thermoautotroiphicus, Methanocaldococcus fervens, Methanocaldococcus indicus, Methanocaldococcus infernus, Methanocaldococcus jannaschii, or

Methanocaldococcus vulcanius.

218. The process of any of claims 201 to 217, wherein the hydrogenotrophic microorganism is chosen from Methanococcus or Methanosarcina.

219. The process of claim 218, wherein the hydrogenotrophic microorganism is a Methanococcus species.

220. The process of claim 218, wherein the hydrogenotrophic microorganism is a Methanosarcina species.

221. The process of any one of claims 201 to 220, wherein the process is continuous, batch, or fed batch.

222. The process of any one of claims 201 to 221 , wherein the process is continuous.

223. The process of any one of claims 201 to 222, wherein the bioreactor is a stirred tank, packed bed, one liquid phase, two liquid phase, hollow fiber membrane, bubble column bioreactor, trickle bed bioreactor (fixed or packed bed), air lift, loop, or fluidized bed bioreactor.

224. The process of any one of claims 201 to 223, wherein the concentration of the hydrogenotrophic microorganism in the bioreactor is about 1 g/L to about 100 g/L.

225. The process of any one of claims 201 to 224, wherein the temperature inside the bioreactor is about 25°C to about 85°C and the pH is from about 6.5 to 7.5.

226. The process of any one of claims 201 to 225, wherein the pressure inside the bioreactor is greater than about 1 bar absolute.

227. The process any one of claims 201 to 226, wherein the amount of CO in the gaseous mixture is no more than about 35%.

228. The process of any one of claims 201 to 226, wherein the amount of CO in the gaseous mixture is no more than about 8%.

229. The process of any one of claims 201 to 228, wherein the ratio of CGs to h½ in the gaseous mixture ranges from about 1 : 50 to about 10:1 , respectively.

230. The process of any one of claims 201 to 229, wherein the nitrogen source comprises ammonia or an ammonia derivative.

231. The process of any one of claims 201 to 230, wherein the sulfur source is present and comprises a sulfide or a sulfide derivative.

232. The process of any one of claims 201 to 231 , wherein the gaseous mixture, sulfur source and the nitrogen source are not mixed together before entering the bioreactor.

233. The process of any one of claims 201 to 231 , wherein the nitrogen source and the sulfur source, and optionally the gaseous mixture, are mixed together before entering the bioreactor.

234. The process of any one of claims 201 to 233, further comprising removing a gas stream from the bioreactor, the gas stream having at least one compound chosen from a sulfur containing compound, a nitrogen containing compound, H2, COx, and a hydrocarbon compound, where x is 1 or 2.

235. The process of any one of claims 201 to 234, wherein the gas stream removed from the bioreactor comprises a combination of at least two of H2, H2S, NH3, CO, CO2 and methane.

236. The process of claim 235, wherein the gas stream is recycled back to one or both of the one or more reactors or the bioreactor.

237. The process of any of claims 234 to 236, wherein after the gas stream leaves the bioreactor it enters a separation device that removes at least some of the H2S, CO2 or both from the gas stream.

238. The process of claim 237, wherein the separation device contains a catalyst.

239. The process of claim 234, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

240. The process of claim 234, wherein after the gas stream leaves the bioreactor it enters at least two separation devices wherein the separation devices remove at least some of the H2S, CO2 and H2 from the gas stream before the gas stream is recycled back to one or both of the one or more reactors or bioreactor.

241. The process of claim 240, wherein H2 is removed from the gas stream by a H2 separation device before the gas stream enters the bioreactor or after the gas stream leaves the bioreactor or a combination of both.

242. The process of any of claims 239 to 241 , wherein the H2 separation device comprises a pressure swing adsorption unit or a hydrogen membrane.

243. The process of any of claims 239 to 241 , wherein the H2 separation device is a hydrogen membrane.

244. The process of any of claims 201 to 243, wherein the gas stream is pressurized before being recycled back to one or both of the one or more reactors or bioreactor.

245. The process of any of claims 201 to 244, further comprising separating the liquid stream to produce a retentate comprising a concentrated amount of the

hydrogenotrophic microorganisms and a filtrate comprising a reduced amount of the hydrogenotrophic microorganisms one or more fermentation product in fermentation broth.

246. The process of claim 245, wherein from about 1 % to 3% by weight of the retentate is removed as purge prior to recycling the retentate back to the bioreactor.

247. The process of claim 245 or 246, wherein the liquid stream is separated using microfiltration.

248. The process of any of claims 245 to 247, wherein the one or more fermentation product is purified from the filtrate to form a fermentation product depleted filtrate fraction.

249. The process of 248, wherein the one or more fermentation product is purified via a process chosen from extraction, drying, chromatography, crystallization, dialysis, solvent extraction, or a combination thereof.

250. The process of any one of claims 201 to 249, wherein the fermentation product is an amino acid.

251. The process of claim 250, wherein the amino acid is at least one chosen from lysine, threonine, glycine and methionine.

252. The process of any one of claims 201 to 249, wherein the fermentation product is an alcohol, aldehyde or ketone.

253. The process or a system of claim 252, wherein the alcohol, aldehyde or ketone is at least one chosen from glycerol, hydroxyacetone, isopropanol, methanol, or phenol.

254. The process of any one of claims 201 to 249, wherein the fermentation product is a carboxylic acid.

255. The process or system of claim 254, wherein the carboxylic acid is at least one chosen from acetate, butyrate, formate, fumarate, isobutyrate, isovalerate, malonate, propionate, or succinate.

256. The process of any one of claims 201 to 249, wherein the fermentation product is a hydroxy acid or a keto acid.

257. The process or system of claim 256, wherein the hydroxy or keto acid is at least one chosen from 2-hydroxybutyrate, 2-hydroxyisobutyrate, 2-hydroxyisovalerate, 2- hydroxyvalerate, 2-hydroxy-3-methylvalerate, 2-oxoisocaproate, 3-hydroxybutyrate, 3- hydroxyisovalerate, 3-methyl-2-oxovalerate, 4 hydroxybenzoate, 4- hydroxyphenyllactate, glycerate, glycolate, lactate, or pyruvate.