NZ716079B2 - Processing of Biomass Materials - Google Patents

Abstract

method comprising combining a cellulolytic microorganism with an inductant comprising a first quantity of a lignocellulosic material, treated with a dose of less than 40 Mrad of bombardment with electrons, and providing conditions that induce the cellulolytic microorganism to produce a cellulase complex tailored to saccharify the particular lignocellulosic material. The relative concentrations of the one or more enzymes is modulated by selection of the particular dose of bombardment with electrons. Subsequently a second quantity of the lignocellulosic material is saccharified with the enzymes, which has been treated with at least 40 Mrad of electron bombardment to reduce its recalcitrance. Wherein the first quantity of the lignocellulosic material has a greater portion of crystalline cellulose than the second quantity and wherein the cellulase complex exhibits enhanced saccharification of the second quantity of the lignocellulosic material attributable, at least in part, to endoglucanase derived from the first quantity of the lignocellulosic material having a greater portion of crystalline cellulose than the second quantity. omplex tailored to saccharify the particular lignocellulosic material. The relative concentrations of the one or more enzymes is modulated by selection of the particular dose of bombardment with electrons. Subsequently a second quantity of the lignocellulosic material is saccharified with the enzymes, which has been treated with at least 40 Mrad of electron bombardment to reduce its recalcitrance. Wherein the first quantity of the lignocellulosic material has a greater portion of crystalline cellulose than the second quantity and wherein the cellulase complex exhibits enhanced saccharification of the second quantity of the lignocellulosic material attributable, at least in part, to endoglucanase derived from the first quantity of the lignocellulosic material having a greater portion of crystalline cellulose than the second quantity.

Description

PROCESSING OF BIOMASS MATERIALS by Marshall , Thomas Craig Masterman, Aiichiro Yoshida, Jennifer Moon Yee Fung, James J. Lynch CROSS REFERENCE TO RELATED APPLICATIONS This application claims the benefit of US. Provisional Application Nos. 61/579,550 and 61/579,562, both filed on December 22, 2011. The entire disclosures of the above applications are incorporated herein by reference.

FIELD OF THE INVENTION The ion pertains to the ation enzymes useful in the processing of biomass materials. For example, the invention relates to producing cellulase enzymes or other enzyme types.

BACKGROUND As demand for petroleum increases, so too does interest in renewable feedstocks for manufacturing biofuels and biochemicals. The use of lignocellulosic biomass as a ock for such cturing processes has been studied since the 1970s. Lignocellulosic biomass is attractive because it is nt, renewable, domestically ed, and does not compete with food industry uses.

Many potential lignocellulosic feedstocks are available today, including agricultural residues, woody biomass, municipal waste, oilseeds/cakes and sea weeds, to name a few. At present these materials are either used as animal feed, post materials, are burned in a cogeneration facility or are landfilled.

Lignocellulosic biomass is recalcitrant to degradation as the plant cell walls have a structure that is rigid and compact. The structure comprises crystalline cellulose fibrils embedded in a hemicellulose matrix, surrounded by lignin. This compact matrix is difficult to access by enzymes and other chemical, biochemical and biological processes. Cellulosic biomass materials (e.g., s al from which substantially all the lignin has been removed) can be more accessible to enzymes and other conversion processes, but even so, naturally-occurring cellulosic materials often have low yields (relative to theoretical yields) when contacted with hydrolyzing enzymes. Lignocellulosic biomass is even more recalcitrant to enzyme attack. rmore, each type of ellulosic biomass has its own specific composition of cellulose, llulose and lignin.

While a number of methods have been tried to extract structural carbohydrates from lignocellulosic biomass, they are either are too expensive, produce too low a yield, leave undesirable chemicals in the resulting product, or simply degrade the sugars.

Saccharides from renewable biomass s could become the basis of chemical and fuels industries by replacing, supplementing or substituting petroleum and other fossil feedstocks. However, techniques need to be developed that will make these monosaccharides available in large quantities and at able es and prices.

SUMMARY OF THE INVENTION Provided herein are methods of ng the production of one or more enzymes by a microorganism, through the use of an inductant.

In one aspect, a method is provided that es combining a cellulosic or lignocellulosic biomass, which has been treated to reduce its recalcitrance, with a microorganism, to induce the production of one or more enzyme(s) by the microorganism by maintaining the microorganism-biomass combination under conditions that allow for the production of the enzyme(s) by the microorganism. In some implementations, the enzyme(s) are then used to saccharify cellulosic or lignocellulosic s.

Also provided herein is a method for inducing the production of an enzyme by a microorganism, where the method includes: providing a first cellulosic or lignocellulosic biomass; ng the first s with a treatment method to reduce its itrance, thereby producing a first treated biomass; providing a microorganism; providing a liquid medium; combining the first treated biomass, the microorganism, and the liquid medium, thereby producing a microorganism-biomass combination; and ining the microorganism-biomass combination under conditions allowing for the production of an enzyme by the microorganism, y producing an inductant-enzyme combination; thereby inducing the production of the enzyme by the microorganism.

Also provided herein is a composition that includes a liquid medium, a cellulosic or lignocellulosic biomass treated to reduce its recalcitrance, a microorganism, and one or more enzymes made by the microorganism. [0011A] Also provided herein is a method comprising: selectively combining a cellulolytic microorganism with an inductant comprising a first quantity of a particular lignocellulosic material, the first quantity of the particular lignocellulosic material having been treated with a particular dose of bombardment with electrons, the dose being selected from the range of less than 40 Mrad, and providing conditions effective to induce the cellulolytic rganism to produce a cellulase complex sing one or more enzymes having ve concentrations tailored to saccharify the particular lignocellulosic material, the relative concentrations of the one or more enzymes being modulated by selection of the particular dose of dment with electrons; and subsequently saccharifying a second quantity of the ular lignocellulosic al with the one or more enzymes, wherein the second quantity of the particular ellulosic material has been treated with at least 40 Mrad of electron dment to reduce its recalcitrance; wherein the first quantity of the ular lignocellulosic material has a greater portion of lline ose than the second quantity, the dose of electron bombardment applied to the first quantity being less than the dose of electron bombardment applied to the second quantity; and wherein the cellulase complex exhibits enhanced saccharification of the second quantity of the particular lignocellulosic material attributable, at least in part, to endoglucanase derived from the first quantity of the particular lignocellulosic material having a greater portion of crystalline cellulose than the second quantity.

In any of the methods or compositions provided herein, the treatment for ng the itrance of the biomass material(s) can be any of: bombardment with electrons, tion, oxidation, pyrolysis, steam explosion, chemical treatment, mechanical treatment, and freeze grinding. Preferably, the treatment method is bombardment with electrons.

The methods and compositions can also include mechanically treating the first or the second cellulosic or lignocellulosic biomass to reduce its bulk density and/or increase its surface area. The biomass material(s) can be comminuted before being combined with the microorganism and liquid medium. The comminution can be dry milling or wet miling. The biomass material can have a particle size of about to 1400 µm.

In any of the methods and compositions described herein, any of the cellulosic or lignocellulosic biomasses can be: paper, paper ts, paper waste, paper pulp, ted papers, loaded papers, coated papers, filled papers, magazines, printed , r paper, polycoated paper, card stock, cardboard, paperboard, cotton, wood, le board, forestry wastes, sawdust, aspen wood, wood chips, grasses, switchgrass, miscanthus, cord grass, reed canary grass, grain residues, rice hulls, oat hulls, wheat chaff, barley hulls, ltural waste, silage, canola straw, wheat straw, barley straw, oat straw, rice straw, jute, hemp, flax, bamboo, sisal, abaca, corn cobs, corn stover, soybean stover, corn fiber, alfalfa, hay, coconut hair, sugar processing residues, bagasse, beet pulp, agave bagasse, algae, seaweed, manure, sewage, offal, agricultural or industrial waste, arracacha, buckwheat, banana, barley, cassava, kudzu, oca, sago, sorghum, potato, sweet potato, taro, yams, beans, favas, lentils, peas, or mixtures of any of these. Alternatively, the cellulosic or lignocellulosic s can include material that was ing after a prior cellulosic or lignocellulosic biomass was previously ted to a product by an enzyme of a microorganism.

In these methods and compositions, the microorganism can be any of a fungus, a bacterium, or a yeast. The microorganism can actually be a population of different microorganisms. The microorganism can be a strain that produces high levels of ase, and/or it can be genetically engineered. The microorganism can be Trichoderma reesei, or it can be Clostrz'dz'um thermocellum, for example. The microorganism can be a T. reesez' strain such as 14, PC3—7, QM9414 or RUT-C30.

In any of these methods and compositions, the cellulosic or lignocellulosic biomass can be combined with the microorganism at a time when the microorganism is in lag phase.

The s and compositions can also include removing all or a portion of the liquid from the microorganism-inductant-enzyme combination, to produce an enzyme extract.

The methods and compositions can also include concentrating one or more of the enzymes, and/or isolating one or more of the enzymes.

The methods and compositions can also include allowing saccharification of the second osic or lignocellulosic biomass to occur, so that one or more sugars are produced.

The one or more sugars can be isolated and/or trated.

It should be understood that this invention is not d to the embodiments disclosed in this Summary, and it is intended to cover ations that are within the spirit and scope of the invention, as defined by the claims.

BRIEF DESCRIPTION OF THE DRAWINGS The foregoing will be apparent from the following more particular description of example embodiments of the invention, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments of the present invention. is a m illustrating the enzymatic hydrolysis of cellulose to glucose.

Cellulosic ate (A) is converted by endocellulase (i) to cellulose (B), which is converted by exocellulase (ii) to iose (C), which is ted to glucose (D) by cellobiase (beta- glucosidase) (iii). is a flow diagram illustrating conversion of a biomass feedstock to one or more products. Feedstock is physically ated (e.g, to reduce its size) (200), optionally treated to reduce its recalcitrance (210), rified to form a sugar solution (220), the solution is transported (230) to a manufacturing plant (e.g., by pipeline, railcar) (or if saccharification is performed en route, the feedstock, enzyme and water is transported), the saccharified feedstock is bio-processed to produce a desired product (e.g., alcohol) (240), and the product can be processed further, e.g., by distillation, to produce a final product (250). Treatment for recalcitrance can be modified by measuring lignin content (201) and setting or adjusting process parameters (205). Saccharifying the feedstock (220) can be modified by mixing the feedstock with medium and the enzyme (221). is a flow m illustrating the treatment of a first biomass (300), on of a cellulase producing organism (310), addition of a second biomass (320), and processing the resulting sugars to make products (e.g, alcohol(s), pure sugars) (330). The first treated s can optionally be split, and a portion added as the second biomass (A). is a flow diagram illustrating the tion of enzymes. A cellulase- producing organism is added to growth medium (400), a treated first biomass (405) is added (A) to make a mixture (410), a second biomass is added (420), and the resulting sugars are processed to make products (e.g., alcohol(s), pure ) (430). Portions of the first biomass (405) can also be added (B) to the second biomass (420). shows results of protein is using SDS PAGE.

DETAILED DESCRIPTION Provided herein are methods of inducing the production of one or more enzymes by a microorganism, through the use of an inductant. The inductant is made from biomass (cellulosic or lignocellulosic) that has been treated to reduce its recalcitrance. The treatment method can include subjecting the biomass to bombardment with electrons, sonication, oxidation, sis, steam explosion, chemical treatment, mechanical treatment, or freeze grinding. As disclosed herein, biomass that has been treated with such a method can be ed with a microorganism in a medium (such as a liquid medium), to induce the microorganism to produce one or more In one aspect, the invention features a method that includes contacting an inducer comprising a lignocellulosic material with a microorganism to produce an enzyme.

Specifically, the processes described herein include saccharifying cellulosic and/or lignocellulosic materials using enzymes that have been produced by Trichoderma ’ fungi, as will be discussed in further detail below.

In general, the invention relates to improvements in sing s als (e.g, biomass als or biomass-derived materials) to produce intermediates and products, such as fuels and/or other products. For example, the processes may be used to produce sugars, alcohols (such as ethanol, isobutanol, or n-butanol), sugar alcohols (such as itol), or c acids.

The invention also relates to the preparation of enzymes useful in the processing of biomass materials. For example the ion relates to ing cellulase enzymes or other enzyme types.

A typical biomass resource contains ose, hemicellulose, and lignin plus lesser amounts of ns, extractables and minerals. The complex carbohydrates contained in the cellulose and hemicellulose fractions can be converted into sugars, e.g., fermentable sugars, by saccharification, and the sugars can then be used as an end product or an intermediate, or converted by fiarther sing, e.g., fermentation or hydrogenation, into a variety of products, such as alcohols or c acids. The product obtained depends upon the method or microorganism utilized and the conditions under which the bioprocessing occurs.

In one embodiment, for instance, the invention es a method of inducing the production of an enzyme. A osic or lignocellulosic s is provided, treated to reduce its recalcitrance, and then ed with a microorganism in a liquid medium. The resulting microorganism—biomass combination is then maintained under conditions allowing for the grth ofthe organism and production of enzymes capable of degrading the biomass. The treated biomass acts as an inductant, causing the rganism to produce enzymes. The method produces an inductant-enzyme combination.

Without wishing to be bound by any theory, it is believed that the treatment used to reduce the recalcitrance of the biomass is important in enzyme induction. The inventors have found that low levels of treatment result in either low levels of enzyme induction, or extremely long lag times, presumably because it is difficult for the microorganisms to extract sugars from the treated biomass material. rly, very high levels of treatment also cause the microorganisms to produce low levels of s, possibly because relatively easy extraction of sugars from the treated biomass lessens the need for the microorganisms to produce large amounts of enzymes.

On a related matter, the recalcitrance treatment also serves to sterilize the material.

Biomass material, by its nature, contains contaminating microbes, which are often embedded deep within the al itself. Because the enzyme inductions as disclosed herein tend to be long fermentations (up to a week or more), sterilization is important. It would therefore be advantageous to treat the material as heavily as possible to ize it. However, such high levels of treatment would likely be counterproductive because high levels of treatment lessen the enzyme production by the microorganisms.

As sed herein, there is therefore a large benefit to be gained from carefully balancing the level of treatment to sterilize the material, yet not over-treat the al so that the microorganisms fail to produce large amounts of enzyme.

The term “inductant,” as used herein, means a osic or lignocellulosic biomass that encourages an organism to produce enzyme. An example would be biomass that has been treated to reduce its recalcitrance. The treated biomass is then used as an enzyme inductant, by being combined with one or more microorganisms in a liquid medium, and then being maintained under conditions that allow the microorganism to produce one or more enzymes.

The inductant-enzyme combination can then be combined with another biomass, and used to saccharify it.

Surprisingly, it has been found that treating the biomass before inoculating it with the microorganism causes an increased amount of s to be produced by the microbes. In addition, different enzymes are ed on the treated biomass, ve to the use of untreated biomass.

As described herein, the cellulosic or lignocellulosic biomass can be d from a wide variety of materials. In one embodiment, the biomass can be lignin hulls. By “lignin hulls,” as used herein, is meant material that is remaining after a biomass has been saccharified.

In certain ments, the invention relates to processes for saccharifying a cellulosic or lignocellulosic material using an enzyme that has been produced by a , e. g., by strains of the cellulolytic filamentous fungus Trichoderma reesez‘. In some implementations, high-yielding cellulase mutants of Trichoderma read are used, e.g., RUT-NG14, PC3-7, QM9414 and/or RUT-C30. Such s are described, for example, in “Selective Screening Methods for the Isolation of High Yielding Cellulase Mutants of Trichoderma reesei,” Montenecourt, BS. and igh, D.E. Adv. Chem. Ser. 181, 1 (1979). These mutants are hyperproducing and are catabolite repression-resistant, allowing high yields of cellulases to be achieved.

In preferred embodiments, the enzyme production is conducted in the presence of a portion of the lignocellulosic material to be saccharified. The lignocellulosic material can act in the enzyme production process as an inducer for cellulase synthesis, producing a cellulase complex having an activity that is tailored to the particular lignocellulosic material. In some implementations, the recalcitrance of the lignocellulosic material is reduced prior to using it as an inducer. It is believed that this makes the cellulose within the ellulosic al more readily available to the fungus. Reducing the recalcitrance of the lignocellulosic material also facilitates saccharification.

In some cases, reducing the recalcitrance of the lignocellulosic material includes treating the lignocellulosic material with a al treatment. The physical treatment can be, for example, radiation, e.g., electron bombardment, sonication, pyrolysis, oxidation, steam explosion, chemical treatment, or ations of any of these treatments. The treatments can also include any one or more of the treatments sed herein, applied alone or in any desired combination, and applied once or multiple times.

Enzymes and s—destroying organisms that break down biomass, such as the cellulose and/or the lignin portions of the biomass, contain or manufacture s cellulolytic enzymes (cellulases), ligninases or various small molecule biomass-destroying metabolites.

These enzymes may be a x of enzymes that act synergistically to degrade crystalline cellulose or the lignin portions of biomass. Examples of cellulolytic enzymes include: ucanases, cellobiohydrolases, and cellobiases (beta-glucosidases).

As shown in for example, during saccharification a cellulosic substrate (A) is initially hydrolyzed by endoglucanases (i) at random locations producing oligomeric intermediates (e.g., cellulose) (B). These intermediates are then substrates for exo-splitting ases (ii) such as cellobiohydrolase to produce cellobiose from the ends of the cellulose polymer. Cellobiose is a soluble 1,4-linked dimer of glucose. y cellobiase (iii) cleaves cellobiose (C) to yield glucose (D). Therefore, the endoglucanases are particularly effective in ing the lline portions of cellulose and increasing the effectiveness of exocellulases to produce cellobiose, which then es the specificity of the cellobiose to produce glucose. Therefore, it is evident that depending on the nature and structure of the cellulosic substrate, the amount and type of the three different enzymes may need to be modified.

The s produced and used in the ses described herein can be produced by a fiingus, e.g, by one or more strains of the fungus Trichoderma reesez‘. In red implementations, high—yielding cellulase mutants of Trichoderma reesei, e.g, RUT—NG14, PC3- 7, QM9414 and/or RUT-C30, are used.

It is preferred that enzyme production be conducted in the presence of a portion of the feedstock that will be rified, thereby producing a cellulase complex that is tailored to the ular feedstock. The feedstock may be treated prior to such use to reduce its recalcitrance, e.g. one or more of the recalcitrance-reducing ses described herein, so as to make , using the cellulose in the feedstock more y available to the fungus.

In a preferred embodiment the enzyme-inducing biomass can be treated by electron dment. The biomass can be treated, for instance, by electron bombardment with a total dose of less than about 1 Mrad, less than about 2 Mrad, than about 5, about 10, about , less 20, about 50, about 100 or about 150 Mrad. Preferably, the enzyme-inducing biomass is treated with a total dose of about 0.1 Mrad to about 150 Mrad, about 1 to about 100 Mrad, preferably about 2 to about 50 Mrad, or about 5 to about 40 Mrad.

As will be discussed further below, once the enzyme has been produced, it is used to saccharify the ing feedstock that has not been used to produce the enzyme. The process for converting the feedstock to a desired product or intermediate generally includes other steps in addition to this saccharification step.

For example, referring to a process for manufacturing an alcohol can include, for example, optionally mechanically treating a ock, e.g. to reduce its size (200), before and/or after this treatment, optionally treating the feedstock with another physical treatment to further reduce its recalcitrance (210), then saccharifying the feedstock, using the enzyme complex, to form a sugar solution (220). ally, the method may also include transporting, e.g. truck or barge, the solution (or the feedstock, enzyme and water, if , by pipeline, railcar, saccharification is performed en route) to a manufacturing plant (230). In some cases the rified feedstock is r bioprocessed (e.g., fermented) to produce a desired product e.g., alcohol (240). This resulting product may in some implementations be processed further, e.g, by distillation (250), to produce a final product. One method of reducing the recalcitrance of the feedstock is by electron bombardment of the feedstock. If desired, the steps of measuring lignin content of the feedstock (201) and setting or adjusting process parameters based on this 2012/071091 measurement (205) can be performed at various stages of the process, as described in US. Pat.

App. Pub. 2010/0203495 A1 by Medoff and Masterman, published August 12, 2010, the complete disclosure of which is incorporated herein by reference. Saccharifying the feedstock (220) can also be modified by mixing the feedstock with medium and the enzyme (221).

The manufacture of the enzyme complexes will now be described first, followed by a description of the method steps discussed above with reference to and the materials used in the process.

A number of different conditions were tested, and the results are as follows. In one embodiment, the enzyme induction biomass is corn cob. In this embodiment, the s is treated by electron bombardment with a 35 Mrad on beam. Preferably, the biomass is comminuted to a particle size of 0 um, more preferably less than 200 um, most preferably less than 50 um. The treated biomass (in either wet or dry form) is added in a total amount of about 25 to about 133 g/L of inoculated medium, more preferably 100 g/L. The inductant biomass can be added at any point in the growth of the microorganisms up through the third day after inoculation, but is ably added 1-3 days after inoculation. The total amount of biomass to be added as an inductant can be added all at once, or in aliquots, for instance, in two parts, or in five parts. Preferably the corncob biomass is added all at once.

The enzyme induction biomass can be presented to the rganisms as a solid, or as a slurry. Preferably it is added as a .

ENZYME PRODUCTION Filamentous fungi, or bacteria that produce cellulase, lly require a carbon source and an inducer for production of cellulase. Without being bound by any theory, it is believed that the enzymes of this disclosure are ularly suited for saccharification of the substrate used for inducing its production.

Lignocellulosic materials comprise ent combinations of ose, hemicellulose and lignin. Cellulose is a linear polymer of e forming a fairly stiff linear structure without cant coiling. Due to this structure and the disposition of hydroxyl groups that can hydrogen bond, cellulose contains crystalline and non-crystalline portions. The crystalline portions can also be of different types, noted as I(alpha) and I(beta) for example, depending on the location of hydrogen bonds between strands. The polymer lengths themselves can vary lending more y to the form of the ose. Hemicellulose is any of several heteropolymers, such as xylan, glucuronoxylan, arabinoxylans, and xyloglucan. The primary sugar monomer present is xylose, although other monomers such as mannose, galactose, rhamnose, arabinose and glucose are present. Typically hemicellulose forms branched structures with lower molecular weights than cellulose. Hemicellulose is therefore an amorphous material that is generally susceptible to enzymatic hydrolysis. Lignin is a complex high molecular weight polymer generally. Although all lignins show variation in their composition, they have been described as an amorphous dendritic network polymer of phenyl propene units. The amounts of cellulose, hemicellulose and lignin in a specific biomaterial depends on the source of the biomaterial. For example wood derived biomaterial can be about 38-49% cellulose, 7—26% hemicellulose and 23-34% lignin depending on the type. Grasses typically are 33-38% cellulose, 24-32% hemicellulose and 17-22% lignin. Clearly ellulosic biomass constitutes a large class of substrates.

The diversity of biomass materials may be further increased by pretreatment, for example, by changing the crystallinity and molecular s of the polymers.

The cellulase producing organism when contacted with a s will tend to produce enzymes that release molecules advantageous to the organism’s growth, such as glucose.

This is done through the phenomenon of enzyme induction as described above. Since there are a variety of substrates in a particular biomaterial, there are a y of cellulases, for example, the endoglucanase, exoglucanase and cellobiase discussed usly. By selecting a particular lignocellulosic material as the inducer the relative concentrations and/or activities of these enzymes can be modulated so that the ing enzyme complex will work efficiently on the lignocellulosic material used as the r or a similar material. For example, a biomaterial with a higher n of crystalline cellulose may induce a more effective or higher amount of endoglucanase than a biomaterial with little crystalline cellulose.

Therefore, there may be many methods for optimal formation and use of ases.

Some s of these ses will be described with reference to the .

For example, referring to a first biomass is optionally pre-treated (300), for example to reduce its recalcitrance, and is then mixed with an aqueous medium and a cellulase producing organism (310). After an adequate time has passed for the cells to grow to a desired stage and enough s have been produced, a second biomass is added (320). The action of the enzyme on the second and any remaining first biomass produces a mix of sugars, which can be further processed to useful products (e.g., alcohols, pure ) (330). The first and second biomass can be portions of the same biomass source material. For example, a portion of the biomass can be combined with the cellulase producing organism and then another portion added at a later stage (A) once some of the enzymes have been produced. Optionally, the first and second biomass may both be ated to reduce recalcitrance. The aqueous media will be discussed below. ing now to the cellulase producing organism (400) can be grown in a growth medium for a time to reach a specific growth phase. For example, this growth period could extend over a period of days or even weeks. Pretreated first biomass (405) can then be contacted (A) with the enzyme producing cells (410) so that after a time enzymes are produced.

Enzyme production may also take place over an extended period of time. The enzyme containing solution is then combined with a second biomass (420). The action of the enzyme on the second and remaining first biomass produces mixed sugars which can be further processed to useful products (430). The first and second s can be portions of the same biomass or could be r but not identical (e.g., ated and non-pretreated) material (B).

In addition to the s discussed above in the cellulase producing organism (400) may optionally be harvested prior to being combined with the first pretreated biomass (410). Harvesting may include partial or almost complete removal of the solvent and growth media components. For example the cells may be collected by centrifugation and then washed with water or another solution.

In another embodiment, after the enzyme(s) is produced (410), it can be concentrated (e.g, between steps 410 and 420 of . Concentration may be by any useful method including chromatography, centrifugation, filtration, is, extraction, evaporation of solvents, spray drying and adsorption onto a solid support. The concentrated enzyme can be stored for a time and then be used by on of a second biomass (420) and tion of useful products (430).

The s media used in the above described methods can contain added yeast extract, corn steep, peptones, amino acids, ammonium salts, phosphate salts, potassium salts, magnesium salts, calcium salts, iron salts, manganese salts, zinc salts and cobalt salts. In addition to these components, the growth media typically contains 0 to 10% glucose (e.g., l to 2012/071091 % glucose) as a carbon source. Additionally the inducer media can n, in addition to the biomass discussed previously, other inducers. For example, some known inducers are lactose, pure cellulose and sophorose. Various components can be added and removed during the processing to optimize the desired tion of useful products.

The concentration of the biomass typically used for inducing enzyme production is r than or equal to 0.1 wt.% and less than or equal to 50 wt.%, greater than or equal to 0.5 wt.% and less than or equal to 25 wt.%, greater than or equal to 1 wt. %, and less than or equal to wt.%, and greater than or equal to 1 wt.% and less than or equal to 10 wt. %.

Any of the processes described above may be performed as a batch, a fed-batch or a continuous process. The processes are useful for ally industrial scale tion, 6.g. having a culture medium of at least 50 liters, preferably at least 100 liters, more preferably at least 500 liters, even more preferably at least 1,000 liters, in particular at least 5,000 liters 0 liters or 500,000 liters. The process may be carried out aerobically or anaerobically.

Some enzymes are produced by submerged cultivation and some by e cultivation.

In any of the process described above, the enzyme can be manufactured and stored and then used to saccharify at a later date and/or different location.

Any of the processes described above may be conducted with agitation. In some cases, agitation may be performed using jet mixing as described in US. Pat. App. Pub. 2010/0297705 A1 by Medoff and Masterman, published November 25, 2010, US. Pat. App.

Pub. 2012/0091035 A1 to Medoff and Masterman, published April 19, 2012, and US. Pat. App.

Pub. 100572 A1 by Medoff and Masterman, published April 26, 2012, the full disclosures of which are incorporated by reference herein.

Temperatures for the growth of enzyme producing organisms are chosen to enhance organism growth. For example for Trichoderma reesei the optimal ature is generally between 20 and 40°C (e.g., 30°C), The temperature for enzyme tion is optimized for that part of the process. For example for Trichoderma reesez’ the optimal ature for enzyme production is between 20 and 40°C (e.g., 27°C).

FEEDSTOCK, BIOMASS MATERIALS, AND/OR INDUCERS The feedstock, which may also be the inducer for enzyme production, is preferably a lignocellulosic material, although the processes described herein may also be used with osic materials, e.g., paper, paper products, paper pulp, cotton, and mixtures of any of these, and other types of biomass. The processes described herein are particularly useful with lignocellulosic materials, because these processes are particularly effective in reducing the recalcitrance of lignocellulosic materials and allowing such materials to be processed into ts and intermediates in an economically viable manner.

As used herein, the term “biomass materials” includes lignocellulosic, osic, y, and microbial materials.

Preferably the enzyme—inducing biomass materials are agricultural waste such as corn cobs, more preferably corn stover. Most preferably, the enzyme-inducing biomass material comprises grasses.

Lignocellulosic materials include, but are not limited to, wood, particle board, forestry wastes (e.g., sawdust, aspen wood, wood chips), grasses, (e.g., switchgrass, miscanthus, cord grass, reed canary grass), grain residues, (e.g, rice hulls, oat hulls, wheat chaff, barley hulls), agricultural waste (e.g., silage, canola straw, wheat straw, barley straw, oat straw, rice straw, jute, hemp, flax, , sisal, abaca, corn cobs, corn stover, soybean stover, corn fiber, alfalfa, hay, t hair), sugar processing residues (e.g., bagasse, beet pulp, agave bagasse), algae, seaweed, manure, sewage, and es of any of these.

In some cases, the lignocellulosic material includes comcobs. Ground or hammermilled comcobs can be spread in a layer of relatively uniform thickness for irradiation, and after irradiation are easy to disperse in the medium for further processing. To facilitate t and collection, in some cases the entire corn plant is used, ing the corn stalk, corn kernels, and in some cases even the root system of the plant.

Advantageously, no additional nutrients (other than a nitrogen , e.g, urea or a) are required during fermentation of comcobs or cellulosic or lignocellulosic materials containing significant amounts of comcobs.

Corncobs, before and after comminution, are also easier to convey and se, and have a lesser tendency to form explosive mixtures in air than other cellulosic or lignocellulosic materials such as hay and grasses.

Cellulosic materials include, for example, paper, paper products, paper waste, paper pulp, pigmented papers, loaded papers, coated papers, filled papers, magazines, printed matter (e.g, books, catalogs, manuals, labels, calendars, ng cards, brochures, prospectuses, newsprint), printer paper, polycoated paper, card stock, cardboard, paperboard, materials having a high alpha-cellulose content such as cotton, and mixtures of any of these. For example paper products as described in US. App. No. 13/396,365 (“Magazine ocks” by Medoff et al., filed February 14, 2012), the fill disclosure of which is incorporated herein by nce.

Cellulosic materials can also e ellulosic materials which have been de— lignified.

Starchy materials include starch itself, e.g., corn starch, wheat starch, potato starch or rice starch, a derivative of starch, or a material that includes starch, such as an edible food product or a crop. For example, the starchy material can be arracacha, buckwheat, , barley, cassava, kudzu, oca, sago, sorghum, regular household potatoes, sweet potato, taro, yams, or one or more beans, such as favas, lentils or peas. Blends of any two or more starchy materials are also starchy materials. Mixtures of starchy, cellulosic and or lignocellulosic materials can also be used. For example, a biomass can be an entire plant, a part of a plant or different parts of a plant, e. g., a wheat plant, cotton plant, a corn plant, rice plant or a tree. The y materials can be d by any of the methods described herein.

Microbial materials include, but are not limited to, any lly occurring or cally modified microorganism or organism that contains or is capable of providing a source of carbohydrates (e.g, cellulose), for example, protists, e.g., animal protists (e.g, protozoa such as flagellates, amoeboids, ciliates, and oa) and plant protists (e.g., algae such alveolates, chlorarachniophytes, cryptomonads, euglenids, phytes, haptophytes, red algae, stramenopiles, and viridaeplantae). Other examples include seaweed, plankton (e.g., macroplankton, mesoplankton, microplankton, nanoplankton, picoplankton, and femptoplankton), phytoplankton, bacteria (e.g., gram positive ia, gram negative bacteria, and extremophiles), yeast and/or es of these. In some instances, microbial biomass can be obtained from natural sources, e.g., the ocean, lakes, bodies of water, e.g., salt water or fresh water, or on land. Alternatively or in addition, microbial biomass can be obtained from culture systems, e.g, large scale dry and wet culture and fermentation systems.

The biomass material can also include offal, and similar sources of material.

In other embodiments, the biomass materials, such as cellulosic, starchy and lignocellulosic feedstock materials, can be obtained from transgenic rganisms and plants that have been modified with respect to a wild type variety. Such modifications may be, for example, through the iterative steps of selection and breeding to obtain d traits in a plant.

Furthermore, the plants can have had genetic material removed, modified, silenced and/or added with respect to the wild type variety. For e, cally d plants can be produced by recombinant DNA methods, where genetic modifications include introducing or modifying specific genes from parental varieties, or, for example, by using transgenic breeding wherein a c gene or genes are introduced to a plant from a ent species of plant and/or bacteria.

Another way to create genetic ion is through on ng wherein new alleles are artificially created from endogenous genes. The artificial genes can be created by a variety of ways including treating the plant or seeds with, for example, al mutagens (e.g., using alkylating agents, epoxides, alkaloids, peroxides, formaldehyde), irradiation (e.g., X-rays, gamma rays, neutrons, beta particles, alpha particles, protons, deuterons, UV radiation) and temperature shocking or other al stressing and subsequent selection techniques. Other methods of providing modified genes is through error prone PCR and DNA shuffling followed by insertion of the desired modified DNA into the desired plant or seed. Methods of introducing the desired genetic variation in the seed or plant include, for example, the use of a bacterial carrier, biolistics, m phosphate precipitation, electroporation, gene splicing, gene silencing, lipofection, microinjection and viral carriers. Additional genetically modified materials have been described in US. Application Serial No 13/396,369 filed February 14, 2012 the full disclosure of which is incorporated herein by reference.

Any of the methods described herein can be practiced with mixtures of any s materials described herein.

BIOMASS -- MECHANICAL ATION Mechanical treatments of the feedstock may include, for example, cutting, milling, e.g., hammermilling, wet milling, grinding, pressing, shearing or chopping. The initial mechanical ent step may, in some implementations, include reducing the size of the feedstock. In some cases, loose feedstock (e.g, recycled paper or switchgrass) is initially prepared by cutting, shearing and/or shredding.

In addition to this size reduction, which can be performed initially and/or later during processing, mechanical ent can also be advantageous for “opening up, ,3 CEstressing,” breaking or ring the feedstock materials, making the cellulose of the materials more tible to chain scission and/or disruption of crystalline structure during the structural modification treatment.

Methods of mechanically treating the feedstock include, for example, g or grinding. Milling may be performed using, for example, a hammer mill, ball mill, d mill, conical or cone mill, disk mill, edge mill, Wiley mill or grist mill. ng may be performed using, for example, a g/impact type grinder. Specific examples of grinders include stone grinders, pin grinders, coffee grinders, and burr rs. Grinding or milling may be ed, for example, by a reciprocating pin or other element, as is the case in a pin mill. Other mechanical treatment methods include mechanical ripping or tearing, other s that apply pressure to the fibers, and air attrition milling. Suitable mechanical treatments further include any other technique that continues the disruption of the internal structure of the material that was initiated by the previous processing steps.

Mechanical treatments that may be used, and the characteristics of the mechanically treated feedstocks, are described in further detail in US. Serial No. 13/276,192, filed r 18, 2011, and published on April 26, 2012 as US. Pat. App. Pub. 2012/0100577 Al, the fiill disclosure of which is hereby incorporated herein by reference.

BIOMASS TREATMENT -- ELECTRON DMENT In some cases, the feedstock may be treated with electron bombardment to modify its structure and thereby reduce its recalcitrance. Such treatment may, for example, reduce the average molecular weight of the feedstock, change the crystalline structure of the feedstock, and/or increase the surface area and/or porosity of the feedstock.

Electron bombardment Via an electron beam is generally preferred, e it provides very high throughput and because the use of a relatively low voltage/high power electron beam device eliminates the need for expensive concrete vault shielding, as such s are “self-shielded” and e a safe, efficient process. While the “self-shielded” devices do include ing (e.g., metal plate shielding), they do not require the uction of a concrete vault, greatly reducing capital expenditure and often allowing an existing manufacturing facility to be used without expensive modification. Electron beam accelerators are available, for example, from IBA (Ion Beam Applications, Louvain-la-Neuve, Belgium), Titan Corporation (San Diego, California, USA), and NHV Corporation (Nippon High Voltage, Japan). 2012/071091 Electron bombardment may be performed using an electron beam device that has a nominal energy of less than 10 MeV, e.g, less than 7 MeV, less than 5 MeV, or less than 2 MeV, e.g., from about 0.5 to 1.5 MeV, from about 0.8 to 1.8 MeV, from about 0.7 to 1 MeV, or from about 1 to about 3 MeV. In some entations the nominal energy is about 500 to 800 keV.

The electron beam may have a relatively high total beam power (the combined beam power of all accelerating heads, or, if multiple accelerators are used, of all accelerators and all heads), e.g., at least 25 kW, e.g., at least 30, 40, 50, 60, 65, 70, 80, 100, 125, or 150 kW. In some cases, the power is even as high as 500 kW, 750 kW, or even 1000 kW or more. In some cases the electron beam has a beam power of 1200 kW or more.

This high total beam power is usually achieved by utilizing multiple accelerating heads. For example, the electron beam device may include two, four, or more accelerating heads. The use of multiple heads, each of which has a relatively low beam power, prevents excessive temperature rise in the al, thereby preventing burning of the al, and also increases the mity of the dose through the thickness of the layer of material.

In some entations, it is desirable to cool the material during electron bombardment. For e, the material can be cooled while it is being conveyed, for example by a screw extruder or other conveying equipment.

To reduce the energy required by the recalcitrance-reducing process, it is desirable to treat the material as quickly as possible. In general, it is preferred that treatment be performed at a dose rate of greater than about 0.25 Mrad per second, e.g, greater than about 0.5, 0.75, 1, 1.5, 2, 5, 7, 10, 12, 15, or even greater than about 20 Mrad per second, e.g., about 0.25 to 2 Mrad per second. Higher dose rates generally require higher line speeds, to avoid thermal decomposition of the material. In one implementation, the accelerator is set for 3 MeV, 50 mAmp beam t, and the line speed is 24 feet/minute, for a sample thickness of about 20 mm (e.g., comminuted corn cob material with a bulk density of 0.5 g/cm3).

In some embodiments, electron bombardment is performed until the material receives a total dose of at least 0.5 Mrad, e.g., at least 5, 10, 20, 30 or at least 40 Mrad. In some embodiments, the treatment is performed until the material receives a dose of from about 0.5 Mrad to about 150 Mrad, about 1 Mrad to about 100 Mrad, about 2 Mrad to about 75 Mrad, 10 Mrad to about 50 Mrad, e.g, about 5 Mrad to about 50 Mrad, from about 20 Mrad to about 40 Mrad, about 10 Mrad to about 35 Mrad, or from about 25 Mrad to about 30 Mrad. In some 2012/071091 entations, a total dose of 25 to 35 Mrad is preferred, applied ideally over a couple of seconds, e.g, at 5 Mrad/pass with each pass being applied for about one second. ng a dose of greater than 7 to 8 Mrad/pass can in some cases cause thermal degradation of the feedstock material.

Using le heads as discussed above, the material can be treated in multiple passes, for e, two passes at 10 to 20 Mrad/pass, e.g., 12 to 18 Mrad/pass, separated by a few seconds of cool-down, or three passes of 7 to 12 Mrad/pass, e.g., 9 to 11 Mrad/pass. As discussed above, treating the material with several relatively low doses, rather than one high dose, tends to prevent overheating of the material and also increases dose uniformity through the thickness of the material. In some implementations, the al is stirred or otherwise mixed during or after each pass and then ed into a uniform layer again before the next pass, to r enhance treatment uniformity.

In some embodiments, electrons are accelerated to, for example, a speed of greater than 75 t of the speed of light, e.g, greater than 85, 90, 95, or 99 percent of the speed of light.

In some embodiments, any processing described herein occurs on lignocellulosic material that remains dry as acquired or that has been dried, e.g. heat and/or reduced , using pressure. For e, in some embodiments, the cellulosic and/or lignocellulosic material has less than about five percent by weight retained water, measured at 25°C and at fifty percent relative humidity.

Electron bombardment can be applied while the cellulosic and/or lignocellulosic material is exposed to air, oxygen—enriched air, or even oxygen itself, or blanketed by an inert gas such as en, argon, or helium. When maximum oxidation is desired, an oxidizing environment is utilized, such as air or oxygen and the distance from the beam source is optimized to maximize reactive gas formation, e.g., ozone and/or oxides of nitrogen.

BIOMASS TREATMENT -— SONICATION, SIS, OXIDATION, STEAM EXPLOSION If desired, one or more sonication, pyrolysis, oxidative, or steam explosion processes can be used in addition to or instead of electron bombardment to reduce the recalcitrance of the feedstock. These processes are described in detail in US. Pat. No. 7,932,065 to Medoff, the full disclosure of which is incorporated herein by reference.

USE OF TREATED S MATERIAL The biomass material (e.g., plant biomass, animal biomass, paper, and municipal waste biomass) can be used as ock to produce useful intermediates and products such as organic acids, salts of organic acids, ides, esters of organic acids and fuels, e.g, fuels for internal combustion engines or feedstocks for fuel cells. Systems and processes are described herein that can use as feedstock cellulosic and/or lignocellulosic materials that are readily available, but often can be difficult to s, e.g, municipal waste streams and waste paper streams, such as streams that include newspaper, kraft paper, corrugated paper or mixtures of these.

In order to convert the feedstock to a form that can be readily processed, the glucan- or xylan-containing cellulose in the feedstock can be hydrolyzed to low molecular weight carbohydrates, such as , by a saccharifying agent, e.g., an enzyme or acid, a process referred to as rification. The low molecular weight carbohydrates can then be used, for example, in an existing manufacturing plant, such as a single cell protein plant, an enzyme manufacturing plant, or a fuel plant, e.g., an ethanol manufacturing facility.

The feedstock can be yzed using an enzyme, e.g., by combining the materials and the enzyme in a solvent, e.g, in an aqueous solution. The enzymes can be made/induced according to the methods described herein.

Specifically, the enzymes can be supplied by organisms that are capable of breaking down biomass (such as the cellulose and/or the lignin portions of the biomass), or that contain or manufacture s cellulolytic enzymes (cellulases), ligninases or various small molecule biomass—degrading metabolites. These enzymes may be a x of enzymes that act synergistically to degrade crystalline cellulose or the lignin portions of biomass. Examples of cellulolytic s include: endoglucanases, cellobiohydrolases, and cellobiases (beta- glucosidases).

During saccharification a osic substrate can be initially hydrolyzed by endoglucanases at random locations producing eric intermediates. These intermediates are then substrates for litting glucanases such as iohydrolase to produce cellobiose from the ends of the cellulose polymer. Cellobiose is a water—soluble 1,4—linked dimer of glucose. y, iase cleaves cellobiose to yield glucose. The efficiency (e.g., time to hydrolyze and/or completeness of hydrolysis) of this s depends on the recalcitrance of the cellulosic material.

INTERMEDIATES AND PRODUCTS Using the processes described herein, the biomass material can be converted to one or more products, such as energy, fuels, foods and materials. c examples of products include, but are not limited to, hydrogen, sugars (e.g, glucose, xylose, arabinose, mannose, galactose, fructose, disaccharides, oligosaccharides and polysaccharides), alcohols (e.g, monohydric ls or dihydric alcohols, such as ethanol, n—propanol, isobutanol, sec-butanol, tert-butanol or n-butanol), ed or hydrous alcohols (e.g., containing greater than 10%, 20%, % or even greater than 40% water), biodiesel, organic acids, hydrocarbons (e.g. , methane, ethane, propane, isobutene, pentane, ne, biodiesel, bio-gasoline and mixtures f), co- products (e.g., proteins, such as cellulolytic proteins (enzymes) or single cell proteins), and mixtures of any of these in any ation or relative concentration, and optionally in ation with any additives (e.g, fuel additives). Other examples include ylic acids, salts of a carboxylic acid, a mixture of carboxylic acids and salts of carboxylic acids and esters of carboxylic acids (e.g., methyl, ethyl and n-propyl esters), ketones (e.g., acetone), des (e.g., acetaldehyde), alpha and beta unsaturated acids (e.g., acrylic acid) and olefins (e.g., ethylene).

Other alcohols and alcohol tives include propanol, propylene glycol, l,4-butanediol, 1,3- ediol, sugar alcohols and polyols (e.g., glycol, glycerol, erythritol, threitol, arabitol, xylitol, ribitol, mannitol, sorbitol, galactitol, iditol, inositol, volemitol, isomalt, maltitol, lactitol, maltotriitol, maltotetraitol, and polyglycitol and other polyols), and methyl or ethyl esters of any of these alcohols. Other products include methyl te, methacrylate, lactic acid, citric acid, formic acid, acetic acid, propionic acid, butyric acid, succinic acid, valeric acid, caproic acid, 3-hydroxypropionic acid, palmitic acid, stearic acid, oxalic acid, malonic acid, glutaric acid, oleic acid, linoleic acid, glycolic acid, gamma-hydroxybutyric acid, and mixtures thereof, salts of any of these acids, mixtures of any of the acids and their respective salts.

Any combination of the above products with each other, and/or of the above products with other products, which other products may be made by the processes described herein or otherwise, may be packaged together and sold as products. The products may be combined, e.g., mixed, blended or co-dissolved, or may simply be ed or sold together.

Any of the products or combinations of products bed herein may be sanitized or sterilized prior to selling the products, e. g., after purification or isolation or even after packaging, to neutralize one or more potentially undesirable contaminants that could be t in the product(s). Such sanitation can be done with electron bombardment, for example, be at a dosage of less than about 20 Mrad, e.g., from about 0.1 to 15 Mrad, from about 0.5 to 7 Mrad, or from about 1 to 3 Mrad.

The processes described herein can produce various by-product streams useful for generating steam and electricity to be used in other parts of the plant (co-generation) or sold on the open market. For example, steam generated from burning by-product s can be used in a lation process. As another example, electricity ted from burning duct s can be used to power electron beam generators used in pretreatment.

The by—products used to generate steam and electricity are derived from a number of sources throughout the process. For example, anaerobic digestion of ater can produce a biogas high in methane and a small amount ofwaste biomass (sludge). As another example, post-saccharification and/or post-distillate solids (e.g., unconverted lignin, cellulose, and hemicellulose remaining from the pretreatment and primary processes) can be used, e.g., burned, as a fuel.

Many ofthe products obtained, such as ethanol or n-butanol, can be utilized as a filel for powering cars, trucks, tractors, ships or trains, e.g., as an internal combustion fuel or as a fuel cell feedstock. Many of the products obtained can also be utilized to power aircraft, such as , e. g., having jet engines or helicopters. In addition, the products described herein can be utilized for electrical power generation, e.g., in a tional steam generating plant or in a fuel cell plant.

Other intermediates and products, including food and ceutical products, are described in US. Pat. App. Pub. 2010/0124583 A1, published May 20, 2010, to Medoff, the full disclosure of which is hereby incorporated by reference herein.

RIFICATION The reduced-recalcitrance feedstock is treated with the enzymes discussed above, generally by ing the material and the enzyme in a fluid medium, e.g., an aqueous solution. In some cases, the ock is boiled, steeped, or cooked in hot water prior to saccharification, as described in US. Pat. App. Pub. 2012/0100577 A1 by Medoff and Masterman, published on April 26, 2012, the entire contents of which are incorporated herein.

The saccharification process can be partially or completely med in a tank (e.g., a tank having a volume of at least 4000, 40,000, or 500,000 L) in a manufacturing plant, and/or can be partially or completely performed in transit, e.g, in a rail car, tanker truck, or in a supertanker or the hold of a ship. The time required for complete saccharification will depend on the process conditions and the biomass material and enzyme used. If saccharification is med in a manufacturing plant under controlled conditions, the cellulose may be substantially entirely converted to sugar, e.g., glucose in about 12-96 hours. If saccharification is performed lly or completely in transit, saccharification may take longer.

It is generally preferred that the tank contents be mixed during sacchariflcation, e.g., using jet mixing as described in International App. No. l , filed May 18, 2010, which was published in English as W0 2010/135380 and designated the United States, the full disclosure of which is incorporated by reference herein.

The addition of surfactants can e the rate of saccharification. Examples of surfactants include non-ionic surfactants, such as a Tween® 20 or Tween® 80 polyethylene glycol surfactants, ionic surfactants, or amphoteric surfactants.

It is generally preferred that the concentration of the sugar solution resulting from saccharification be relatively high, e.g, greater than 40%, or greater than 50, 60, 70, 80, 90 or even greater than 95% by weight. Water may be d, e.g., by evaporation, to increase the concentration of the sugar solution. This reduces the volume to be shipped, and also inhibits microbial growth in the solution.

Alternatively, sugar solutions of lower concentrations may be used, in which case it may be desirable to add an crobial ve, e.g. , a broad spectrum antibiotic, in a low concentration, e.g., 50 to 150 ppm. Other le antibiotics include amphotericin B, ampicillin, chloramphenicol, ciprofloxacin, icin, hygromycin B, kanamycin, neomycin, penicillin, puromycin, streptomycin. Antibiotics will inhibit growth ofmicroorganisms during transport and e, and can be used at appropriate concentrations, e.g., between 15 and 1000 ppm by weight, e.g., between 25 and 500 ppm, or between 50 and 150 ppm. If d, an antibiotic can be included even if the sugar concentration is relatively high. Alternatively, other additives with anti-microbial of preservative properties may be used. Preferably the antimicrobial additive(s) are food-grade.

A relatively high concentration solution can be obtained by limiting the amount of water added to the biomass material with the enzyme. The concentration can be controlled, e.g. by controlling how much rification takes place. For example, concentration can be increased by adding more biomass material to the solution. In order to keep the sugar that is being produced in solution, a surfactant can be added, e.g., one of those discussed above.

Solubility can also be increased by increasing the temperature of the on. For example, the solution can be maintained at a temperature of 40-50°C, 60—80°C, or even .

SACCHARIFYING AGENTS Suitable cellulolytic enzymes include ases from species in the genera Bacillus, CaprinuS, Myceliophthora, Cephalosporz'um, Scytalz'dl'um, Penicillium, AspergilluS, Pseudomonas, Humicola, um, Thielavz'a, Acremonz’um, ChrySOSporz'um and Trichoderma, especially those produced by a strain selected from the species ASpergz’lluS (see, e.g., EP Pub.

No. 0 458 162), Humicola insolens ssified as Scytalz'dz'um thermophilum, see, e.g., US. Pat.

No. 4,435,307), CaprinuS cinereuS, um oxysporum, Myceliophthora thermophila, Merz’pz'luS giganteus, Thielavia terrestris, nium Sp. (including, but not limited to, A. persicinum, A. acremonium, A. brachypenium, A. dichromosporum, A. obclavatum, A. pinkertoniae, A. roseogriseum, A. incoloratum, and A. furatum). Preferred strains include Humicola insolens DSM 1800, Fusarium oxySporum DSM 2672, Mycelz'ophthora thermophila CBS 117.65, osporz'um Sp. RYM-202, Acremonium Sp. CBS 478.94, Acremonium Sp.

CBS , Acremonium perSicz'num CBS 169.65, Acremonium acremom’um AHU 9519, Cephalosporium Sp. CBS , Acremonium brachypenium CBS 866.73, Acremanium dichromosporum CBS , Acremonium obclavatum CBS 311.74, Acremom’um pinkertoniae CBS 157.70, Acremonium roseogriseum CBS 134.56, Acremonium ratum CBS 146.62, and Acremoniumfuratum CBS 299.70H. Cellulolytic enzymes may also be obtained from ChrySOSporium, preferably a strain of Chrysosporium lucknowense. Additional strains that can be used include, but are not limited to, derma (particularly T. , T. reesez', and T. koningii), alkalophilic Bacillus (see, for example, US. Pat. No. 3,844,890 and EP Pub. No. 0 458 162), and Streptomyces (see, e.g., EP Pub. No. 0 458 162).

Many microorganisms that can be used to saccharify biomass material and produce sugars can also be used to ferment and convert those sugars to useful products.

SUGARS In the processes described , for example after saccharification, sugars (e.g. glucose and xylose) can be isolated. For example sugars can be isolated by precipitation, crystallization, chromatography (e.g, simulated moving bed chromatography, high pressure chromatography), fiagation, extraction, any other isolation method known in the art, and combinations thereof.

HYDROGENATION AND OTHER CHEMICAL ORMATIONS The processes described herein can include hydrogenation. For example glucose and xylose can be hydrogenated to sorbitol and xylitol respectively. Hydrogenation can be accomplished by use of a catalyst (e.g., Pt/gamma-A1203, Ru/C, Raney Nickel, or other catalysts know in the art) in combination with H2 under high pressure (e.g., 10 to 12000 psi). Other types of chemical transformation of the products from the ses described herein can be used, for example production of c sugar derived products such (e.g., furfural and al-derived products). Chemical transformations of sugar derived products are described in U.S. Prov. App.

No. 61/667,481, filed July 3, 2012, the disclosure of which is incorporated herein by nce in its entirety.

TATION The sugars produced by saccharification can be isolated as a final product, or can be fermented to produce other products, e.g, alcohols, sugar alcohols, such as erythritol, or organic acids, e.g., lactic, glutamic or citric acids or amino acids.

Yeast and Zymomonas bacteria, for example, can be used for fermentation or conversion of sugar(s) to alcohol(s). Other microorganisms are discussed below. The optimum pH for fermentations is about pH 4 to 7. For example, the optimum pH for yeast is from about pH 4 to 5, while the optimum pH for Zymomonas is from about pH 5 to 6. Typical fermentation times are about 24 to 168 hours (e.g., 24 to 96 hrs) with temperatures in the range of 20°C to 40°C (e.g., 26°C to 40°C), however thermophilic microorganisms prefer higher temperatures.

In some embodiments, e.g., when anaerobic organisms are used, at least a portion of the fermentation is conducted in the absence of oxygen, e.g., under a blanket of an inert gas such as N2, Ar, He, C02 or mixtures thereof. Additionally, the mixture may have a constant purge of an inert gas flowing through the tank during part of or all of the fermentation. In some cases, anaerobic condition, can be achieved or maintained by carbon dioxide production during the fermentation and no additional inert gas is needed.

In some embodiments, all or a portion of the fermentation process can be interrupted before the low molecular weight sugar is completely converted to a product (e.g., ethanol). The intermediate fermentation ts include sugar and ydrates in high trations. The sugars and carbohydrates can be ed via any means known in the art. These intermediate fermentation products can be used in preparation of food for human or animal ption.

Additionally or alternatively, the intermediate fermentation products can be ground to a fine particle size in a stainless-steel laboratory mill to produce a flour—like substance.

Jet mixing may be used during fermentation, and in some cases saccharification and fermentation are performed in the same tank.

Nutrients for the rganisms may be added during saccharification and/or fermentation, for example the food-based nutrient packages bed in US. Pat. App. Pub. 2012/0052536, filed July 15, 2011, the complete disclosure of which is incorporated herein by reference.

“Fermentation” includes the methods and products that are disclosed in US. Prov.

App. No. 61/579,559, filed December 22, 2012, and US. Prov. App. No. 61/579,576, filed December 22, 2012, the contents of both of which are orated by reference herein in their entirety.

Mobile fermenters can be utilized, as described in International App. No.

PCT/U82007/074028 (which was filed July 20, 2007, was published in h as WO 2008/01 1598 and designated the United States), the ts of which is incorporated herein in its entirety. Similarly, the saccharification equipment can be mobile. Further, saccharification and/or tation may be performed in part or entirely during transit.

FERMENTATION AGENTS The rganism(s) used in fermentation can be naturally-occurring microorganisms and/or engineered microorganisms. For example, the rganism can be a bacterium ding, but not limited to, e.g., a olytic bacterium), a fungus, (including, but not limited to, e.g., a , a plant, a protist, e.g. a protozoa or a fungus-like protest (including, but not limited to, e.g., a slime mold), or an alga. When the organisms are compatible, mixtures of organisms can be utilized.

Suitable fermenting microorganisms have the y to convert ydrates, such as glucose, fructose, xylose, arabinose, mannose, galactose, oligosaccharides or polysaccharides into fermentation products. Fermenting microorganisms include strains of the genus Saccharomyces spp. (including, but not d to, S. cerevisiae (baker’s yeast), S. distatz'cas, S. avaram), the genus Klayveromyces, (including, but not limited to, K. marxianas, K. fragilis), the genus a (including, but not limited to, C. pseudotropicalz’s, and C. brassz'cae), Pichz'a stz‘pz‘tz’s (a relative of Candida ae), the genus Clavz'spora (including, but not limited to, C. lusz'tanz'ae and C. opantz'ae), the genus Pachysolen (including, but not limited to, P. tannophilas), the genus Bretannomyces (including, but not limited to, e.g., B. clausenz'z' (Philippidis, G. P., 1996, Cellulose bioconversion technology, in Handbook on Bioethanol: Production and Utilization, Wyman, C.E., ed., Taylor & Francis, Washington, DC, 179-212)). Other le microorganisms include, for example, Zymomonas mobilis, Clostrz’dz’um spp. (including, but not limited to, C. thermocellum (Philippidis, 1996, supra), C. robulylacetonicum, C. saccharobalylz‘cum, C. Paniceum, C. bez’jernckl‘z', and C. acetobulyll‘cum), Monilz'ella pollinz's, Monilz'ella megachz'lz'ensis, Lactobacz'llus spp. Yarrowz'a lipolytica, Aureobasidz'um sp., sporonoz'des 319., Trigonopsis variabilis, sporon sp., Monilz'ellaacetoabatans Sp.

Typhala variabilis, a magnoliae, Ustilaginomycetes Sp., Pseudozyma tsukabaensis, yeast species of genera Zygosaccharomyces, Debaryomyces, Hansenula and Pichia, and fungi of the dematioid genus Torula.

For instance, Clostrz'dz'um spp. can be used to produce ethanol, butanol, butyric acid, acetic acid, and acetone. Lactobacz'llus spp., can be used to produce lactice acid.

Many such microbial strains are publicly available, either commercially or through depositories such as the ATCC (American Type Culture Collection, Manassas, Virginia, USA), the NRRL (Agricultural Research Sevice Culture Collection, Peoria, Illinois, USA), or the DSMZ che Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany), to name a few.

Commercially available yeasts include, for example, Red Star®/Lesaffre Ethanol Red (available from Red Star/Lesaffre, USA), FALI® (available from Fleischmann’s Yeast, a division of Burns Philip Food Inc., USA), SUPERSTART® (available from Alltech, now Lalemand), GERT STRAND® (available from Gert Strand AB, Sweden) and FERMOL® (available from DSM Specialties).

Many microorganisms that can be used to saccharify biomass material and produce sugars can also be used to ferment and convert those sugars to useful products.

DISTILLATION After fermentation, the resulting fluids can be distilled using, for e, a “beer ” to separate ethanol and other ls from the majority of water and residual solids.

The vapor exiting the beer column can be, e.g., 35% by weight ethanol and can be fed to a rectification column. A mixture of nearly azeotropic (92.5%) ethanol and water from the rectification column can be purified to pure (99.5%) ethanol using vapor-phase lar sieves.

The beer column bottoms can be sent to the first effect of a three-effect evaporator. The cation column reflux condenser can e heat for this first effect. After the first effect, solids can be separated using a centrifuge and dried in a rotary dryer. A portion (25%) of the centrifuge effluent can be recycled to tation and the rest sent to the second and third evaporator effects. Most of the evaporator condensate can be returned to the process as fairly clean condensate with a small portion split off to waste water treatment to prevent build-up of low-boiling compounds.

Other than in the examples herein, or unless otherwise expressly ed, all of the numerical ranges, amounts, values and percentages, such as those for amounts of materials, tal contents, times and temperatures of on, ratios of amounts, and others, in the following portion of the specification and attached claims may be read as if ed by the word “about” even though the term “about” may not expressly appear with the value, amount, or range. Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following cation and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an t to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding ques.

Notwithstanding that the numerical ranges and parameters g forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains error arily resulting from the standard ion found in its underlying respective testing measurements. Furthermore, when numerical ranges are set forth , these ranges are inclusive of the recited range end points (i.e., end points may be used). When percentages by weight are used herein, the numerical values reported are ve to the total weight.

Also, it should be understood that any numerical range recited herein is intended to include all sub-ranges subsumed therein. For example, a range of “1 to 10” is intended to include all sub-ranges between (and including) the recited minimum value of 1 and the recited maximum value of 10, that is, having a minimum value equal to or greater than 1 and a maximum value of equal to or less than 10. The terms “one, a, or “an” as used herein are intended to include “at least one” or “one or more,” unless ise indicated.

EXAMPLES Materials & Methods The following ures and materials were used in the following examples.

Cell banking: The following Trichiderma ’ strains were banked: ATCC 66589, PC3-7; ATCC 56765, RUT-C30; ATCC 56767, NG-l4; ATCC 26921, QM 9414.

Each cell was rehydrated and propagated in potato dextrose (PD) media at 25°C.

For production of master cell banks, each strain was rehydrated overnight in 0.5ml sterile water. To propagate cells, 40 ul of rehydrated cells were used to inoculate potato se agar (PDA) solid medium. Rehydrated cells were also inoculated into 50 ml of PD liquid medium and incubated at 25°C and 200 rpm. After 2 weeks culture in PDA media, spores were resuspended in sterile NaCl (9g/L), 20% glycerol solution, and stored in -80°C freezer for use as a cell bank.

WO 96698 Protein measurement and cellalase assay: Protein concentration was measured by the Bradford method using bovine serum albumin as a standard.

Filter paper assay (FPU), cellobase activity and CMC activity was carried out using the IUPAC method (T.K. Ghose, Pure Appl. Chem. 59:257-68, 1987).

The reaction product (glucose) was analyzed on a YSI 7100 Multiparameter Bioanalytical System (YSI Life es, Yellow s, Ohio, USA) or HPLC.

Media: The media included com steep (2 g/L), ammonium sulfate (1.4 g/L), potassium ide (0.8 g/L), Phosphoric acid (85%, 4mL/L), phthalic acid dipotassium salt (5 g/L), magnesium sulfate heptahydrate L), calcium chloride (0.3g/L), ferrous e heptahydrate (5 mg/L), manganese sulfate mono hydrate (1.6 mg/L), zinc sulfate heptahydrate (5 mg/L) and cobalt chloride hexahydrate (2mg/L). The media is described in Herpoel-Gimbert et al., Biotechnologyfor Biofaels, 2008, 1:18.

Bio-reactor: The freezer stock from the cell banking was used to make the seed culture using the media described above, with 2.5% additional glucose. The seed culture was typically made in a flask using an incubator set at 30°C and 200rpm for 72hrs. Seed e broth (50mL) was used as an inoculum in the 1L starting medium in a 3L fermenter. In growth phase, 35 g/L of lactose was added to the medium. The e conditions were as follows: 27°C, pH 4.8 (with 6M ammonia), air flow 0.5 VVM, stirring 500 rpm, and dissolved oxygen (DO) was maintained above 40 % oxygen saturation. In the ion phase, the desired inducer (discussed below) was added. During fermentation, Antiform 204 (Sigma) was ed into the culture when the foam reached the fermentor head.

Shakeflask: In addition to the media described above, for the flask culture, Tris buffer (12.1g/L), maleic acid (11.06g/L) and sodium hydroxide (2.08g/L) were added. A starter culture was prepared in the media with added glucose. After 3 days of growth, the cell mass was harvested by centrifugation. The cell mass was re-suspended in 50 m1 of media with the desired inducer. The flasks were placed in a shaker incubator set at an agitation speed of 200 rpm and temperature of 30°C.

Example 1. Cellulase Performance Test on Paper, Treated Corn Cob and Untreated Corn Cob Various inducers (treated biomass (TBM), untreated biomass (UBM), paper (P) and carboxylmethylcellulose (CMC, Aldrich)) were used to produce enzymes. The s (TBM and UBM) was milled corn cob collected n mesh sizes of 15 and 40. Treatment of the s (UBM) to produce the TBM involved electron bombardment with an electron beam to a total dose of 35 Mrad. The paper was ed and screened to have a nominal particle size smaller than 0.16 inch. The r experiments were conducted using shake flasks and PC3-7 and RUT-C30 strains. After 3 days of the growth culture, the harvested cell mass was added to a series of shake flasks each containing 50 ml of medium and 1 wt. % of one of the inducers.

The induction experiment was allowed to proceed for 11 days. The culture supernatant was then harvested by centrifugation at 14,500 rpm for 5 minutes, and stored at 4°C.

Protein concentration ofculture supernatant: Using the cell culture grown in the shake flasks and derived from PC3-7, protein concentrations after 11 days were 1.39, 1.18, 1.06 and 0.26 mg/mL for TBM, UBM, P and CMC tively. For RUT-C30, the protein concentrations were 1.26, 1.26, 1.00 and 0.26 mg/mL for TBM, P, UBM and CMC respectively.

Cellulase ty: The cellulase activities were assessed and are listed in the table below.

Table 1. Cellulase activity for different inducers and cell strains.

Inducer Cell type FPU (U/mL) Cellobiase activity FPU Cellobiase activity /mL U/m U/m TBM PC—3—7 0.57 0.47 1.04 0.86 UBM PC—3—7 0.45 0.39 1.08 0.93 P PC-3—7 0.57 0.39 0.96 0.66 CMC PC7 0.06 0.11 0.55 0.99 TBM RUT-C30 1.02 0.53 1.97 1.03 UBM RUT-C30 0.72 0.42 1.76 1.03 P RUT-C30 0.71 0.40 1.31 0.74 CMC RUT-C30 0.24 0.18 1.77 1.31 These results show that treated biomass serves to induce enzyme production at a greater rate than untreated biomass.

Example 2. Enzyme Production in Different Concentrations ofTBM Inducer This e was done using bioreactors. Cell strain RUT-C30 was propagated in the media with 2.5 % glucose. After 3 days of growth the e was centrifuged and the cells was re-suspended in 50 ml of media with 1, 3, 5, 7 and 9 wt.% TBM. The protein concentrations and activities after 11 days of incubation at 27°C and 200 rpm are shown in the table below.

Table 2. Amounts of Protein and Enzyme Made With Differing Amounts of Inducer r amount (wt.%) n (g/L) FPU (U/mL) CMC (U/mL) 1 0.7 1.4 1.3 2 1.4 3.1 1.7 3.4 6.2 2.6 7 2.9 2.5 1.5 9 1.5 0.6 1.0 These results show that higher levels of enzymes were produced when the treated biomass (TBM) was added at a rate of 5 %.

Saccharification ofbiomass with enzymes: Saccharification of biomass (TBM) using enzymes produced by addition of 2, 5 and 7 wt.% treated biomass inducer (TBM) versus a commercial enzyme (DuetTM Accellerase, Genencor) was conducted. The biomass, 10wt. % TBM, was combined with either 0.25 ml/g of enzyme culture broth or commercial enzyme. The saccharification was carried out at 50°C and 200 rpm in a shaking incubator. After 24 hours the amount of generated glucose was measured by YSI. The amount of e produced per L of solution and mg of protein is shown in the table below.

Table 3. Amount of Glucose Produced From Varying Levels of Inducer Enzyme produced from Glucose (g/L) Glucose (g/mg) 2% TBM r 4.04 2.31 % TBM inducer 4.06 1.08 7% TBM inducer 3.02 0.83 Commercial enzyme 14.4 0.50 Example 3. SDS—PAGE of Enzyme Produced With Treated Biomass A bioreactor culture was prepared using the method described above except that the mixing was done at 50 rpm rather than 500 rpm. The protein assay showed that 3.4 g/L protein was produced.

The is of the protein using SDS PAGE is shown in Lane 1 and 5 are molecular weight markers, Lane 2 is a 30 uL load of the protein, Lane 3 is a 40 uL load of the protein, Lane 4 is DuetTM Accelerase enzyme complex (Genencor).

Example 4. Range of Conditions Tested Induction Parameters Range Working Best Tested Tested Range Range Amount Added 25-133g/L 25-133g/L 100g/L Timing of on Day 0-3 1-3 Day 1-3 Frequency of on 1, 2, and 5 1, 2, and 5 1 Presentation wet or dry wet or dry wet or dry Treatment Levels 35 35 35 e Timing of Addition Day 3 Day 3 Day 3 Amount Added 4.7-40g/L/d 4.7-18.7g/L/d 18.7g/L/d continuous continuous uous Frequency of Addition feed feed feed Any patent, publication, or other disclosure material, in whole or in part, that is said to be incorporated by reference herein is incorporated herein only to the extent that the incorporated material does not conflict with existing definitions, statements, or other disclosure material set forth in this disclosure. As such, and to the extent necessary, the disclosure as explicitly set forth herein supersedes any conflicting material incorporated herein by nce.

Any material, or portion thereof, that is said to be incorporated by reference herein, but which conflicts with existing definitions, ents, or other disclosure material set forth herein will only be incorporated to the extent that no conflict arises between that incorporated material and the existing sure material. 2012/071091 While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made n without departing from the scope of the invention encompassed by the appended claims.

Claims (33)

CLAIMS What is claimed is:

1. A method comprising: selectively combining a cellulolytic rganism with an inductant comprising a first quantity of a particular lignocellulosic material, the first quantity of the particular lignocellulosic material having been d with a particular dose of bombardment with ons, the dose being selected from the range of less than 40 Mrad, and ing conditions effective to induce the cellulolytic microorganism to produce a cellulase complex comprising one or more enzymes having relative concentrations tailored to saccharify the particular lignocellulosic al, the relative concentrations of the one or more enzymes being modulated by selection of the particular dose of bombardment with electrons; and subsequently saccharifying a second quantity of the particular lignocellulosic material with the one or more enzymes, wherein the second quantity of the particular lignocellulosic material has been d with at least 40 Mrad of electron bombardment to reduce its recalcitrance; wherein the first quantity of the ular lignocellulosic material has a greater portion of crystalline cellulose than the second quantity, the dose of electron bombardment applied to the first quantity being less than the dose of electron bombardment applied to the second quantity; n the cellulase complex exhibits enhanced saccharification of the second quantity of the particular lignocellulosic material utable, at least in part, to endoglucanase derived from the first quantity of the particular lignocellulosic material having a greater portion of crystalline cellulose than the second quantity.

2. The method of claim 1, wherein the total dose of electron bombardment d to the first quantity of the particular lignocellulosic material is from 0.5 to 40 Mrad.

3. The method of claim 1 or 2, wherein the total dose of electron bombardment applied to the first quantity is less than about 5 Mrad.

4. The method of any one of claims 1-3, wherein the total dose of electron bombardment applied to the second quantity is from 40 to 150 Mrad.

5. The method of any one of claims 1-4, n the total dose of on bombardment applied to the first quantity is less than about 5 Mrad, and the total dose of electron bombardment applied to the second quantity is 40 to 150 Mrad.

6. The method of any one of claims 1-5, wherein the dose rate of electron bombardment d to the second quantity of the particular lignocellulosic material is from about 0.25 to about 20 ec.

7. The method of any one of claims 1-6, wherein the electron bombardment of the second quantity of the particular lignocellulosic material is provided by an electron beam device having an energy of about 0.5 to about 10 MeV.

8. The method of any one of claims 1-7, wherein the first quantity of the particular lignocellulosic material and/or the second quantity of the particular lignocellulosic material has been mechanically treated to reduce its bulk density and/or increase its surface area.

9. The method of any one of claims 1-8, wherein the first quantity of the particular lignocellulosic material has been comminuted before being combined with the cellulolytic microorganism.

10. The method of any one of claims 1-9, wherein the second quantity of the particular ellulosic material has been comminuted before subsequently saccharifying the second quantity of the particular lignocellulosic material with the one or more enzymes.

11. The method of claim 9 or 10, wherein the comminution comprises dry milling.

12. The method of any one of claims 9-11, n the ution comprises wet milling.

13. The method of any one of claims 1-12, wherein the first quantity of the particular lignocellulosic material and/or the second quantity of the particular lignocellulosic material has a particle size of about 30 to 1400 µm.

14. The method of any one of claims 1-13, wherein the cellulolytic microorganism is selected from the group consisting of a fungus, a bacterium, and a yeast.

15. The method of any one of claims 1-14, wherein the cellulolytic microorganism is a strain of cellulolytic filamentous fungus.

16. The method of any one of claims 1-15, where the cellulolytic microorganism comprises a cellulase producing fungus.

17. The method of any one of claims 1-16, wherein the cellulolytic microorganism is cally engineered.

18. The method of any one of claims 1-17, wherein the cellulolytic rganism is selected from the group consisting of Trichoderma reesei, and Clostridium cellum.

19. The method of any one of claims 1-18, wherein the cellulolytic microorganism is selected from among the strains of Trichoderma .

20. The method of any one of claims 1-19, wherein the cellulolytic microorganism is a lite repression-resistant mutant of Trichoderma reesei.

21. The method of any one of claims 1-20, wherein the olytic microorganism is selected from the group consisting of: RUT-NG 14, PC3-7, QM9414 and/or RUT-C30.

22. The method of any one of claims 1-21, wherein the one or more enzymes are cellulase enzymes.

23. The method of any one of claims 1-22, wherein the one or more enzymes comprise a ase complex of two or more of the following: endoglucanases, cellobiohydrolases, cellobiases, and lulases.

24. The method of any one of claims 1-23, wherein relative concentrations of the one or more enzymes correlates to the relative proportion of one or more substrates in the first quantity of the particular ellulosic material, the one or more substrates comprising one or more of: cellulose, a hemicellulose, and lignin.

25. The method of any one of claims 1-24, wherein the relative proportions of the one or more enzymes correlates to the crystallinity of one or more ates in the first quantity of the particular lignocellulosic material.

26. The method any one of claims 1-25, n the particular lignocellulosic material comprises agricultural residues.

27. The method of any one of claims 1-26, wherein the particular lignocellulosic material comprises one or more of: cotton, grasses, grain residues, rice hulls, oat hulls, wheat chaff, barley hulls, silage, canola straw, wheat straw, barley straw, oat straw, rice straw, jute, hemp, flax, bamboo, sisal, abaca, corn cobs, com stover, soybean stover, corn fiber, a, hay, coconut hair, sugar processing residues, bagasse, beet pulp, agave bagasse, algae, seaweed, cha, buckwheat, banana, barley, cassava, kudzu, oca, sago, m, potato, sweet potato, taro, yams, beans, favas, lentils, peas, and agricultural waste material from any one or more of these.

28. The method of any one of claims 1-27, wherein the particular lignocellulosic material comprises a residue of a rification or fermentation process.

29. The method of any one of claims 1-28, wherein the second quantity of the particular lignocellulosic material comprises material from which the first quantity was selected.

30. The method of any one of claims 1-28, wherein the first quantity of the particular lignocellulosic material was obtained from a different source than the source of the second quantity of the ular ellulosic material.

31. The method of any one of claims 1-30, wherein the electron bombardment of the second quantity of the particular lignocellulosic material is applied in multiple doses.

32. The method of any one of claims 1-31, further comprising concentrating the cellulase complex and storing the cellulase complex prior to subsequently saccharifying the second quantity of the particular lignocellulosic material.

33. The method of claim 32, where concentrating comprises one or more of: chromatography, centrifugation, filtration, dialysis, extraction, evaporation of solvents, spray , and adsorption onto a solid support.