Patent Publication Number: US-2011053228-A1

Title: Microbial processing of cellulosic feedstocks for fuel

Description:
RELATED APPLICATIONS 
     This application claims the benefit of U.S. provisional application Ser. No. 61/272,165, filed Aug. 25, 2009, entitled “Triacylglceride Extraction and Purification Process,” Ser. No. 61/272,244, filed Sep. 3, 2009, entitled “Method and Apparatus for Drying of Biological Materials,” Ser. No. 61/282,824, filed Apr. 7, 2010, entitled “Method and Apparatus for Oxygenating an Aerobic Culture,” and Ser. No. 61/344,218, filed Jun. 14, 2010, entitled “Triacylglyceride Extraction Process with Reduced Energy Consumption,” which are hereby incorporated by reference. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT 
     This invention was made with U.S. government support under one or more of the following contracts: HR0011-09-C-0075 awarded by the U.S. Defense Advanced Research Projects Agency. The U.S. government may have certain rights in the invention. 
    
    
     BACKGROUND 
     1. Field of the Invention 
     The present application generally relates to the use of microbial and chemical systems to convert biomass to commodity chemicals, such as biofuels/biopetrols. 
     2. Related Art 
     Petroleum is facing declining global reserves and contributes to more than 30% of greenhouse gas emissions driving global warming. Annually 800 billion barrels of transportation fuel are consumed globally. Diesel and jet fuels account for greater than 50% of global transportation fuels. 
     Significant legislation has been passed, requiring fuel producers to cap or reduce the carbon emissions from the production and use of transportation fuels. Fuel producers are seeking substantially similar, low net carbon fuels that can be blended and distributed through existing infrastructure (e.g., refineries, pipelines, tankers). 
     Due to increasing petroleum costs and reliance on petrochemical feedstocks, the chemicals industry is also looking for ways to improve margin and price stability, while reducing its environmental footprint. The chemicals industry is striving to develop greener products that are more energy, water, and CO 2  efficient than current products. Fuels produced from biological sources, such as biomass, represent one aspect of the process. 
     SUMMARY 
     A system and method are provided which utilize microbes to convert biomass feedstock into fuel. In one aspect of the invention, a method of producing aromatic compounds and lipids includes receiving a feedstock including biological matter; separating the feedstock into a liquid phase feedstock and a solid phase feedstock; adding water and nutrients to the solid phase feedstock, thereby producing a liquid culture; inoculating the liquid culture with one or more microbes capable of converting the solid phase feedstock into aromatic compounds and lipids, the inoculated liquid culture yielding microbial biomass; providing suitable conditions for the microbes to convert the solid phase feedstock to aromatic compounds and lipids; and extracting produced aromatic compounds and lipids. Lipids are chemically converted to alkanes and related hydrocarbons for fuel, or alternatively are transesterified to produce biodiesel, both using processes known in the art. 
     In another aspect of the invention, the liquid phase feedstock, representing hydrolyzates of the cellulosic and/or hemicellulosic portions of the biological matter, is inoculated with microbes capable of converting the hydrolyzates into lipids. Lipids are chemically converted to alkanes and related hydrocarbons for fuel, or alternatively are transesterified to produce biodiesel, both using processes known in the art. 
     In another aspect of the invention, a system for producing fuel components includes a bioreactor having an inoculated liquid culture including microbes and biomass; and a controller in communication with the bioreactor, the controller providing operating instructions to the bioreactor; and where the bioreactor yields the fuel components. 
     In yet another aspect of the invention, a method of producing aromatic compounds and lipids includes receiving a feedstock including biological matter; adding water and nutrients to the feedstock; inoculating the feedstock with microbes capable of converting a portion of the feedstock into aromatic compounds and lipids; providing suitable conditions for the microbes to convert a portion of the feedstock to aromatic compounds and lipids; and extracting produced aromatic compounds and lipids. 
     Other features and advantages of the invention will be apparent from the following detailed description, the claims and the appended drawings. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The details of the present invention, both as to its structure and operation, may be gleaned in part by study of the accompanying drawings, in which like reference numerals refer to like parts, and in which: 
         FIG. 1  is a flow chart of a cellulosic feedstock pretreatment process according to an embodiment of the invention. 
         FIG. 2  is a schematic of a bioreactor system for oxygenating fluid according to an embodiment of the invention. 
         FIG. 3  is a top view of the bioreactor system of  FIG. 2 . 
         FIG. 4  is a close up of fluid flow ramps, as shown in  FIG. 2 . 
         FIG. 5  is a flow chart of an inoculation and fermentation process according to an embodiment of the invention. 
         FIG. 6  is a flow chart of an inoculation and fermentation process according to an embodiment of the invention. 
         FIGS. 7A and 7B  are block diagrams of a system for drying biomass according to an embodiment of the invention. 
         FIG. 8  is a block diagram of a system for drying biomass according to an alternative embodiment of the invention. 
         FIG. 9  is a flow chart of a microbial biomass collection process according to an embodiment of the invention. 
         FIG. 10A  is a flow chart of a TAG extraction and purification process according to an embodiment of the invention. 
         FIG. 10B  is a flow chart of a TAG extraction and purification process according to another embodiment of the invention. 
         FIG. 11  is a flow chart of a biomass drying process according to an embodiment of the invention. 
         FIG. 12  is a flow chart of a separation process according to an embodiment of the invention. 
         FIG. 13  is a block diagram of process equipment used in accordance with  FIGS. 1-12 . 
     
    
    
     DETAILED DESCRIPTION 
     After reading this description it will become apparent to one skilled in the art how to implement the invention in various alternative embodiments and alternative applications. However, although various embodiments of the present invention will be described herein, it is understood that these embodiments are presented by way of example only, and not limitation. As such, this detailed description of various alternative embodiments should not be construed to limit the scope or breadth of the present invention as set forth in the appended claims. 
     The described embodiments relate to systems and methods for production of liquid biofuel from low-value starting materials. In some embodiments, the systems and methods relate specifically to the production of diesel, gasoline and/or aviation fuel from cellulosic feedstocks. In some embodiments, the method includes a multi-step process that inputs raw feedstock and outputs triacylglyceride (“TAG”) and aromatic compounds. In some embodiments, the systems and methods relate specifically to the production of biodiesel fuel. The production of biodiesel fuel is further described in co-pending application Ser. No. 12/573,732, filed Oct. 5, 2009, entitled “Microbial Processing of Cellulosic Feedstocks for Fuel,” which is incorporated herein by reference. 
     Present methods of converting cellulosic biomass utilize biomasses specifically cultivated for producing biofuels. In addition to these “cultivated cellulosic biomasses”, cellulosic biomass may be obtained from cellulosic waste materials such as sawdust, wood chips, cellulose, algae, other biological materials, municipal solid waste (e.g., paper, cardboard, food waste, garden waste, etc.), and the like. 
     A process in accordance with an embodiment of the present invention includes converting cellulosic waste materials into liquid fuel. In one aspect, cellulosic material such as agricultural waste is converted into lipids such as TAG, using specially selected or developed microbes (e.g., including genetically engineered microbes, competitively bred microbes, etc.). These microbes convert free sugars, cellulose and hemicellulose, major components of plant matter, into TAG. 
     TAG includes three fatty acids linked to a glycerol backbone. When dissociated from the glycerol and hydrotreated, the fatty acids are converted to hydrocarbons, which form the major components of diesel, gasoline and jet fuel. In some embodiments, TAG itself may serve as a component of fuel. A benefit associated with the present process is that no net carbon is added to the atmosphere when the fuel is burned because the feedstock was originally produced by photosynthesis, sequestering carbon dioxide from the atmosphere. 
     Gasoline and jet fuel specifications require, in addition to alkanes, a certain proportion of aromatic compounds. TAG cannot be readily converted to aromatic compounds. However, plant matter also contains lignin, a polymeric agglomeration of aromatic compounds that can be broken down into the aromatics required for fuel. Specialized microbes attack lignin and convert it into smaller, individual aromatic compounds. Thus, microbial conversion processes can suffice to convert agricultural and municipal waste originating from plant matter into all the components of fuel. 
     In accordance with an embodiment of the present invention, a biomass feedstock (e.g., sawdust, wood chips, cellulose, algae, other biological materials, or other solid materials) includes high-molecular-weight, high-energy-content molecules including cellulose, hemicellulose and lignin to be converted into fuel. The feedstock can generally be biological matter, which generally includes organic compounds from plant or other lignocellulosic sources. The resulting fuel may be in fluid form, meaning that gaseous and liquid components may contribute to the make up of the fuel. For example, in one embodiment, the resulting fuel may include methane (gas) and octane (liquid), as well as a variety of other components. The feedstock material may be a low-value or waste material. 
     In certain embodiments of the present invention, a cellulosic biomass feedstock includes at least 10% cellulosic waste materials. In some embodiments, the cellulosic biomass feedstock includes greater than 50% cellulosic waste materials. In still other embodiments, the cellulosic biomass feedstock includes up to 100% cellulosic waste materials. 
     In one aspect, the feedstock may be a biological product of plant origin, thus resulting in no net increase in atmospheric carbon dioxide when the resultant fuel product is combusted. 
     In some embodiments, two or more feedstocks may be used. For example, a secondary feedstock may include any material by-product of a cellulose conversion process, which material is capable of being converted into fuel by microbial action. The secondary feedstock may include glycerol molecules or fragments thereof, or glycerol with additional carbon atoms or short paraffinic chains attached. Such compounds can be produced, for example, when alkanes are cleaved from TAG or when TAG is transesterified to produce biodiesel. 
     For simplicity of explanation, a process in accordance with the present invention may be divided into three main steps: (1) feedstock pretreatment, (2) inoculation and fermentation/digestion, and (3) harvesting and extraction of the TAG and/or aromatic products. 
     (1) Feedstock Pretreatment 
     In an embodiment, raw feedstock is pretreated to make its carbon content accessible to microbial digestion and to kill any naturally present microbes that might compete with the preferred species introduced for the purpose of TAG and/or aromatic compound production. Pretreatment can include three steps: (1) mechanical pretreatment, (2) thermal-chemical pretreatment and heat sterilization and/or ultraviolet (“UV”) irradiation and/or pasteurization, and (3) filtration/separation. In the mechanical pretreatment step, raw feedstock may be conveyed to a chopper, shredder, grinder or other mechanical processor to increase the ratio of surface area to volume. 
     The thermal-chemical pretreatment step can treat the mechanically processed material with a combination of water, heat and pressure. Optionally, acidic or basic additives or enzymes may also be added prior to heat-pressure treatment. This treatment further opens up the solid component (e.g., increases the ratio of surface area to volume) for microbial access and dissolves sugars and other compounds (e.g., dissociates cellulose and hemicellulose into component sugars, dimers and/or oligimers) into a liquid phase to make it more amenable to microbial digestion. Examples of such treatment include the class of processes known variously as hydrolysis or saccharification, but lower-energy processing, such as simple boiling or cooking in water, may also be utilized. 
     In one embodiment, non-carbon microbial nutrients are added prior to the thermal-chemical pretreatment step. Non-carbon microbial nutrients include, for example, sources of nitrogen, phosphorus, sulfur, metals, etc. After adding the non-carbon microbial nutrients, the entirety may then be sterilized, such as via autoclaving. In some embodiments, the non-carbon microbial nutrients are sterilized separately from the sugar components. In some embodiments, the sugar components are not sterilized. 
     The filtration/separation step  140  preferably separates the solid matter (e.g., where the lignin is concentrated) from the liquid (e.g., which contains most of the sugars and polysaccharides from the cellulose and hemicellulose in the feedstock). In some embodiments, the filtration/separation step  140  is optional. Consequently, in these embodiments, the solid matter and liquid remain together throughout processing. 
     In some embodiments, the feedstock is fortified (e.g., via the addition of glycerol.) For example, glycerol used in the feedstock fortification may be obtained as a byproduct of some TAG-to-alkanes conversion processes. Generally, glycerol is released by the conversion of TAG to produce bio-diesel fuel (e.g. via transesterification). The released glycerol may then be metabolized to contribute to TAG formation. A benefit of using the glycerol to form TAG is that it may speed the growth or TAG accumulation of certain microbial species during fermentation, discussed below. It is understood that glycerol obtained from transesterification is not high-purity, but rather includes a variety of constituents. 
     Referring now to  FIG. 1 , a flow chart of a cellulosic feedstock pretreatment process  100  in accordance with an embodiment of the invention is shown. The pretreatment process  100  includes a receiving stage  110  for receiving the cellulosic feedstock and a mechanical pretreatment stage  120  for transforming the feedstock into small particles. 
     The pretreatment process  100  also includes a thermo-chemical pretreatment stage  130  to open up the cellulosic structure, rendering the cellulosic structure more accessible to the microbes and to bring some of the sugars and polysaccharides into solution. In some embodiments, water and, optionally, acidic or basic additives  134  are added to the feedstock during this thermo-chemical pretreatment stage  130 . In some embodiments, non-carbon nutrients  138  used for the microbial metabolization are also added during this thermo-chemical pretreatment stage  130 . In some embodiments, the non-carbon nutrients  138  are sterilized separately from the feedstock in the thermal/chemical pretreatment and sterilization step  130 . Thereafter, the non-carbon nutrients  138  and the feedstock are combined after the solid/liquid separation step  140 . In other embodiments, the non-carbon nutrients and the feedstock are combined prior to the solid/liquid separation step  140 . It should be appreciated that the thermo-chemical treatment step  130  also serves to sterilize the cellulosic material and surrounding liquid to inhibit potentially competing microorganisms. 
     The pretreatment process  100  also includes a solid-liquid separation stage  140  which may use mechanical means such as filters and/or centrifuges to separate the bulk of the solid feedstock from the liquid portion. As described above, the liquid portion  144  includes mostly sugars and polysaccharides, while the solid portion  148  includes lignin as well as undissolved cellulose and hemicellulose. 
     (2) Inoculation and Fermentation 
     In the inoculation and fermentation stage, the solid and liquid portions of the treated feedstock are preferably placed in separate digesters. The digesters are vessels containing the feedstock material and microbes which break down the feedstock into lipids or aromatics, respectively, a solvent (e.g., water), and non-carbon nutrients (e.g., nitrates, phosphates, trace metals, and the like). 
     The microbes may be species of any of two classes: one class which converts cellulose, hemicellulose or glycerol into lipids, and a second class which breaks lignin down into aromatic compounds. Microbes including bacterial and/or fungal species which convert cellulose, hemicellulose or glycerol into lipids include, for example, Trichoderma reesi, Acinetobacter sp., and members of the Actinomyces and Streptomyces genera, some of which have been reported to store up to 80% of dry cell mass as lipids. 
     In a preferred embodiment, the fungus used in the cultures and bioprocess reactor processes described herein comprises a cellulose degrading fungus of the genus  Penicillium . In some embodiments, the fungus comprises a fungus of the same species as the isolated  Penicillium menonorum  strain MM-P1 deposited with the Agricultural Research Service Culture Collection (NRRL) on Aug. 2, 2010, having been assigned deposit Accession No: 50410. The address of the depository, NRRL, is 1815 North University Street, Peoria, Ill. 61604. This deposit has been made in full accordance with the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. In a preferred embodiment, the isolated fungus comprises  Penicillium menonorum  and progeny thereof. In another preferred embodiment, the isolated fungus comprises NRRL deposit Accession No: 50410 and progeny thereof. Preferred embodiments of the processes described herein utilize one or more of the organisms described in U.S. provisional application Ser. No. ______, entitled “Bioreactors Comprising Fungal Strains,” filed concurrently herewith and incorporated herein by reference. In an embodiment, the materials, technology, and processes described in “Bioreactors Comprising Fungal Strains,” filed concurrently herewith, may be used in the systems and methods described herein. 
     In some embodiments, other species of bacteria and fungi break lignin down into aromatics. In some embodiments, the microbes are filamentatious or have a filamentatious morphology or structure. This filamentatious morphology often results in chain growth of the microbes, which allows the microbes to be collected in traditional sieves or separation means. 
     In some embodiments, the microbes utilized in inoculation are grown in starter cultures using standard procedures. The standard procedures may vary according to the particular species selected. 
     The resultant lipids may include any molecular forms having a straight-chain saturated hydrocarbon portion. Such lipids are desirable because the straight-chain saturated hydrocarbon portion is relatively easy to convert to vehicle fuel. 
     Lipids include TAGs and wax esters. Mono- or di-unsaturated hydrocarbon chains are also found in lipids and are suitable for conversion to alkanes, albeit with the requirement of additional hydrogen to saturate them. 
     The resultant aromatic compounds include any molecular forms having carbon ring structures. Examples of preferred aromatics include xylenes, methyl benzenes, and others. 
     In some embodiments, TAG and aromatic production is promoted by maintaining the microbes in a high-carbon, low-nitrogen environment, and providing aeration and/or agitation. As is understood, optimizing the percentage of feedstock carbon converted to TAG or aromatics requires controlling the growth of the microbial culture so as to reduce the carbon consumed by cell replication and metabolic activity and to increase the carbon consumed in producing TAG and aromatics. This can be done by controlling the ratio of non-carbon nutrient to carbon in the feedstock, as well as by controlling other parameters such as pH, temperature, dissolved oxygen, carbon dioxide production, fluid shear, and the like. In some embodiments, one or more measurements of these parameters may be used to determine when to harvest produced TAG. For example, in one embodiment, the carbon or nitrogen availability may be changed in order to switch the culture from a rapid growth mode to a TAG accumulation mode. In other words, one or more of these parameters may have a value associated with or which is indicative of desired TAG production. 
     For example, in some embodiments, fluid shear is controlled by either moving the reactor vessel as a whole (e.g., by rocking it back and forth at a controlled frequency) or by means of mechanical agitators immersed in the fluid (e.g., any of a variety of paddle or stirrer shapes driven by electrical motors at a controlled frequency). 
     In some embodiments, aeration or oxygenation of the fluid is accomplished by any number of means, including via entrainment of air due to turbulence caused by mechanical agitation of the fluid and via bubbling or sparging air, air enriched with oxygen, or pure oxygen through the fluid. 
     In some embodiments, oxygenation of the fluid is accomplished by using turbulence to mix oxygen present in the head space of a bioreactor into the liquid medium. As used herein, the head space is the space above the liquid medium that is occupied by gas and vapor. Without wishing to be bound by any particular theory, use of the head space for oxygenating the fluid is believed to result in a significantly reduced cost of operating an aerobic culture. 
     For example, referring to  FIGS. 2-4 , a bioreactor system  200  including a bioreactor vessel  210  with head space  220  is shown. As presented, bioreactor vessel  210  is rotationally symmetric about a vertical axis (not shown). System  200  includes a rotary agitation mechanism  230  along the vertical axis that forces a strongly azimuthal flow when rotated (in accordance with the arrow shown). For example, as shown, the rotary agitation mechanism  230  includes a drive motor  232 , a drive shaft  234 , and a paddle  236 . 
     As shown in  FIG. 2 , a rotary drive motor  232  and drive shaft  234  and a largely vertical paddle  236  induce a strongly azimuthal flow of the liquid medium about the center axis of the vessel  230 . In one embodiment, a flat paddle  236  with a radius equal to about one quarter of the bioreactor vessel  210 &#39;s diameter and rotating at up to 150 revolutions per minute is adequate to drive the desired flow. The clearance between the outer radius of the paddle  236  and the inner edge of the ramps  240  (discussed below) may be minimized, while avoiding impact, rubbing or other physical contact between the two structures. 
     In an alternative embodiment, the agitation paddle  236  may be curved, so as to be concave in the direction of rotation. While not wishing to be bound by any particular theory, this change in paddle shape may generate a stronger azimuthal flow for a given paddle speed. 
     A set of stationary ramps  240  that force fluid to flow along a path with variable vertical displacement are also shown within bioreactor vessel  210 . These ramps  240  may be secured to the vessel  210  via support rods  212  and fasteners  214 . 
     As shown in  FIGS. 2 and 4 , the topmost set of ramps  240  breaks the liquid surface  250  and is designed to cause a substantial fraction of the liquid to flow up the ramp  240  and fall back into the bulk liquid  255 . The turbulent re-entry of this “waterfall” entrains gases from the head space  220  back into the bulk liquid  255 . The lower-level ramps  240  ensure that the gases thus entrained at the surface are well-mixed at all depths in the vessel  210 . 
     In some embodiments, sets of ramps  240  may be used at various depths to deflect the fluid flow in the vertical direction to generate strong fluid mixing vertically. In such embodiments, the topmost set of ramps  240  may extend across the mean liquid surface  250 . It may be desirable to make sure that the topmost ramp&#39;s highest surface is low enough to allow most of the fluid to reach and flow over the top, falling freely back into the liquid  255  and entraining gas from the head space  220 , such as shown in  FIG. 4 . 
     In order to achieve improved results, ramps  240  having ramp angles of 30 to 40 degrees, with the highest point of the topmost ramp  240  extending approximately 3 inches above the mean liquid surface  250  may be used. In such embodiments, the ramp&#39;s width is approximately one quarter of the bioreactor vessel  210 &#39;s diameter, and two stacks of ramps  240  placed diametrically opposite each other may be adequate to achieve the desired mixing and oxygenation. 
     In one embodiment, ramps  240  having two horizontal end plates  240   a,b  and a flat, tilted plate section  240   c  that generates the vertical flow are used. The end plates  240   a,b  may include slots  242  for ease of mounting on vertical support rods  212  fixed in the bioreactor vessel  210  (for example, by being fixed to a top cover plate). The slots  242  may also allow the ramp angle to be adjusted straightforwardly. 
     As shown in  FIG. 2 , two stacks  245   a ,  245   b , of ramps  240  located diametrically opposite each other in the vessel  210  are shown. However, any number of stacks of ramps  240  (e.g., three, four, etc.) may be used. Also, as shown, there are two or three ramps  240  in each stack  245   a ,  245   b.    
     As described above, each ramp  240  includes three planar sections-two horizontal end plates  240   a ,  240   b  and one tilted plate  240   c . The ramp  240  can be made concave, or given raised lips along its inside and outside edges, to form a trough that can send a larger proportion of the liquid over the lip of the waterfall, for increased gas entrainment efficiency. Alternatively, the ramp  240  can be made as a single, continuous, curvilinear form along the azimuthal direction, rather than out of three planar segments. 
     As shown in  FIG. 4 , the ramps  240  are rectangular in shape. In some embodiments, ramps  240  are made as circular arc segments to fit into the circular bioreactor vessel  210 , catch a larger fraction of the azimuthal flow and maintain a constant separation from the paddle  236 . 
     Referring back to  FIG. 2 , support rods  212  may be vertical and threaded for receiving threaded fasteners  214  to mount and hold the ramps  240 . The ramps  240  could equally be attached to the side wall of the bioreactor vessel  210  via fastening means such as welding, adhesives, or through fasteners (e.g., bolts or rivets). In one embodiment, pair of rods  212  is used to support each stack of ramps  240 , however, any number of rods  212  may be used. 
     As shown in  FIG. 2 , the rods  212  are suspended from a top plate (not shown) of the bioreactor vessel  210 . However, rods  212  may alternatively or also be anchored to the bottom of the bioreactor vessel  210 . In some embodiments, the rods  212  are attached to a collapsible mechanism (not shown) that can be inserted through a smaller opening at the top of the vessel  210 . 
     The bioreactor vessel  210  is shown as a flat-bottomed bioreactor. However, the design may be adapted to a conical-bottom bioreactor or a dish-bottom reactor by reducing radii of ramps  240  and the agitation paddle  236  appropriately, as a function of height in the conical or dished portion of the reactor. 
     Paddles  236 , shafts  234 , ramps  240 , rods  212  and fasteners  214  may be made of any material that (a) is strong enough to withstand peak and average loadings experienced in course of operation over time, (b) does not corrode in the aqueous culture with its range of pH and temperature, and (c) does not either interfere with the bioactivity of the culture or suffer biocorrosion. The default material is stainless steel, but many different plastics and metals may be used. 
     In an alternative embodiment, herein referred to as a “fountain reactor”, the reactor simply pumps the aqueous culture into a fountain in the head space, for example, via a spray fan, with the liquid entraining gases as it falls back into the main body of the liquid. The pump can be a submersible, large-diameter pump to avoid clogging or fouling by the biomass generated by the culture. In some embodiments, the pump is mounted outside or external to the reactor. 
     An example illustrating benefits of the bioreactor system  200  will now be described. 
     EXAMPLE 
     Experiments were conducted on two 100-liter microbial cultures that were identical except for the oxygenation mechanism. The first culture (e.g., control sample) used 10 liters per minute of oxygen-enriched air, pumped through a perforated-tube sparger at the bottom of the bioreactor. The second culture (e.g., experimental sample) used the “waterfall” method exemplified by bioreactor system  200  and pumped the same 10 liters per minute of identically enriched air into the headspace. 
     On the fourth day of the culture, at a time of maximal growth (and, hence, maximal oxygen consumption), the dissolved oxygen in the sparged reactor (e.g., control sample) measured 8 to 9 milliliters of O 2  per liter of liquid, while the dissolved oxygen in the waterfall reactor (e.g., experimental sample) measured 17 to 18 milliliters per liter. Based on this example, the waterfall reactor produced a higher dissolved oxygen content (by 8-10 milliliters per liter) than a traditional sparged reactor. 
     In accordance with some embodiments, using the waterfall method includes optionally, enriching the gas in the head space of an aqueous bioreactor by pumping in air enriched with oxygen by a commercially available oxygen enricher. Because the enriched gas is being pumped into a large manifold, there is no requirement of high pressure pumping, in contrast to approaches relying on bubbling (sparging). 
     Benefits of the using the bioreactor vessel  210  and the waterfall method include:
         No high output pressure oxygen enrichment required;   No high-pressure gas flow required;   No perforated or sintered sparging apparatus to suffer biofouling;   No moving parts other than the rotary agitator;   Very low cost;   Highly effective oxygenation of the culture, even under heavy growth conditions that are often susceptible to oxygen deprivation.       

     Referring now to  FIG. 5 , a flow chart of an inoculation and fermentation process  500  in accordance with an embodiment of the invention is shown. The inoculation and fermentation process  500  includes a receiving stage  510  for receiving the liquid output  144  from the pretreatment process  100  and an inoculation step  520  that adds a starter culture  525  of the selected microorganism or microorganisms to the liquid  144  to form a mixture at the inoculation step  520 . The selected microorganisms may be a single species or strain, or a combination of multiple species or strains. 
     The inoculation and fermentation process  500  also includes a metabolization step  530 , which takes the mixture and controls parameters such as temperature, pH, dissolved oxygen, and fluid shear using appropriate methods known in the art. During this metabolization step  530 , the microorganisms proliferate and metabolize the feedstock, creating intracellular inclusions of lipids in the form of triacylglycerides (TAG). At the end of this stage (e.g., as determined by defined values of one or more of the parameters of time, pH, dissolved oxygen or others) the metabolization is stopped, yielding a depleted fluid  540  with suspended microbes containing TAG. 
     Referring now to  FIG. 6 , a flow chart of an inoculation and fermentation process  600  in accordance with an embodiment of the invention is shown. The inoculation and fermentation process  600  includes a receiving stage  610  for receiving the solid portion of the pretreated feedstock  148  from the pretreatment process  100  and an inoculation step  620 , in which the portion of feedstock  148  is mixed with sterilized water and non-carbon nutrients  624  and a starter culture of specially selected microorganisms suited to decomposing the lignin  628 . The selected microorganisms may be a single species or strain, or a combination of multiple species or strains. 
     The inoculation and fermentation process  600  also includes a metabolization step  630 , which takes this mixture and controls parameters such as temperature, pH, dissolved oxygen, and fluid shear using appropriate methods known in the art. During this metabolization step  630 , the microorganisms proliferate and metabolize the feedstock, breaking the lignin down into smaller aromatic compounds that are released into the solution. At the end of this stage (e.g., as determined by defined values of one or more of the parameters of time, pH, dissolved oxygen or others) the metabolization is stopped, yielding a mixture  640  containing depleted solids, microbes, and gas and liquid containing the desired aromatic compounds. 
     (3) Harvesting and Product Extraction 
     Extracting product from a digester is different, depending on whether the product is TAG from cellulose breakdown or aromatic hydrocarbons from lignin breakdown. Each is considered in turn. In both cases, however, choosing the proper time to harvest will maximize yield. Measurements such as pH, dissolved oxygen, carbon dioxide production, remaining carbon nutrient concentration, and the like can be used to determine the optimal harvest time. 
     Harvesting and Extracting TAG 
     The liquid medium in the digesters has provided TAG-producing microbes with nourishment, allowing the microbes to flourish and reproduce. These microbes store TAG in intracellular structures. The first step, accordingly, is to harvest or collect the cellular biomass from the liquid medium. Because cells tend to form multicellular agglomerations hundreds of micrometers in size, harvesting may be performed by screening, sieving, centrifugation, or filtration. The multicellular agglomerations may be the result of the filamentatious nature of the microbes, as discussed above. The result of this step is a mass of cellular biomass with remaining excess water, e.g. wet biomass. 
     In some embodiments, the wet biomass is dried after the collecting step. For example, gross excess water may be removed mechanically from the wet biomass by pressing through a roller press, squeezed, or wrung. The wet biomass may then be further dried using a vacuum oven, lyophilizer, or other common drying equipment. It should be recognized that when using a vacuum oven, for example, the temperature should be controlled so that TAG is not or is only minimally hydrolyzed (e.g., drying at temperatures of about less than 80° C.). In some embodiments, lyophilizing is selected as the drying means because it has the effect of increasing the surface area to volume ratio of the biomass, which makes subsequent extraction quicker. In some embodiments, flash freezing (e.g., via immersion in liquid nitrogen) is used to break up the cell structures, improving efficiency of subsequent extraction, and possibly partially disrupting the cells. 
     Because the wet biomass may be degraded when the water is removed, drying the biomass both efficiently and gently is preferred. In order to achieve gentle drying, processes in accordance with an embodiment generally do not expose or minimize exposure of the biomass to heat. 
     Additionally, when drying biomass, it is important to avoid releasing live microbes or spores into the environment. Consequently, microbial cultivators and processors often ensure that any biological material is sterilized prior to release in the atmosphere, drain or trash. In an embodiment, the described apparatus and method ensure biological material is sterilized, thereby avoiding releasing live contaminants (e.g., microbes or spores) into the environment. 
     In some embodiments, a method of drying the biomass includes exposing the biomass to low-humidity air or dry, inert gas and then sterilizing the air, thereby killing any microbes or spores or other biological material entrained in the air. 
     An exemplary system for drying the biomass is provided in  FIG. 7A . As shown in  FIG. 7A , system  700  includes a dehumidifying chamber  702 , a drying chamber  705 , and a sterilization chamber  707 . System  700  may additionally include a fluid intake section  701 , a fluid pump  703 , and hoses or connectors  704 . Drying chamber  705  may include one or more perforated drying screens  706 . Sterilization chamber  707  may include a sterilization or biocide fluid  708 . As used herein, “fluid” includes gases such as air, as well as liquids. 
     In one embodiment, the system  700  first provides low-humidity air or dry inert gas via fluid intake section  701  and dehumidifying chamber  702 . Then, the dry inert gas or low-humidity air is moved past the biomass to be dried in drying chamber  705 . The air or inert gas is thereafter sterilized in sterilization chamber  707 , thereby killing any microbes or spores or other biological matter entrained in the air. The arrows indicate air flow. 
     As is appreciated, the source of low-humidity air may be a dehumidifier. Alternatively, when a dry, inert gas is used, the source may be a compressed gas cylinder filled with a suitable gas such as nitrogen or helium. 
     Drying chamber  705  may be any container such as a metal or plastic box with sufficient volume to contain the material (e.g., biomass) to be dried. Drying chamber  705  typically includes an input duct or port coupled to the source of low-humidity air (e.g., dehumidifying chamber  702 ), and an output duct or port coupled to the sterilization chamber  707 . The material to be dried may be arranged or spread thinly upon on one or more shelves or platforms (e.g., perforated drying screens  706 ) supported within the drying chamber  705 , preferably arranged so that the air passes freely over the material. The shelves may be porous or grid-like to permit evaporation from both top and bottom surfaces of the material. 
     Referring to  FIG. 7B , in some embodiments, perforated drying screens  706  have a mesh screen  710  placed on top of the drying screens  706 . Thereafter, the biomass may be added to the drying chamber  705  by pumping the biomass into the top of the drying chamber  705  from bioreactor  200  via tubing and/or pump  712 . Air may be bubbled up from beneath the drying screens  706  from an air source  713 , where each perforation  706   a  may have a microchannel  706   b  attaching it to the air source  713  (e.g., a bubbler). In one embodiment, the air source  713  is the same air source as used in  FIG. 7A . The air flowing through the screens  706  helps the liquid to flow out of the biomass and through the mesh  710 . Additionally, in some embodiments, drying chamber  705  includes a stirrer  722  and/or a heater  724  in the space above mesh  710 . While not wishing to be bound by any particular theory, it is believed that stirrer  722  assists the liquid flowing through mesh  710 , while trapping the biomass on mesh  710 , and heater  724  provides drying to the biomass. Any resulting liquid may be pumped out of the bottom of the tank  705  via tubing and/or pump  714  and recycled back into bioreactor  200 . In some embodiments, a dehumidifier and various types of heat can also be used (e.g., heat the air, heat the tank, etc.). 
     Upon reaching a sufficient dryness, the biomass can be removed from drying chamber  705  via traditional mechanical or pneumatic means and/or automated means. For example, suitable removal means include, but are not limited to, scoops, conveyors, valves, and compressed air or vacuum. 
     Additionally, while not explicitly shown, the drying chamber may comprise a tumble-dry configuration whereby the material to be dried is agitated with the low-humidity air. Alternatively, any other drying configuration which results in a moisture content of less than or equal to about 10% may be used. 
     Sterilization chamber  707  may be any container such as a metal or plastic box with sufficient volume to contain the means for sterilizing the air and any entrained biological matter. Sterilization chamber  707  typically includes an input port or duct coupled to the exit port of the drying chamber  705 , and an output port or duct through which sterilized air is released. The output port may include a filter (not shown) to further contain biological material. 
     The sterilizing means may be any means for killing microbes, spores, or other biological matter entrained in the passing air, prior to release. The sterilizing means may be a drum or bucket containing water and bleach through which the air is bubbled. Alternatively, the sterilizing means may be ultraviolet lamps producing radiation with sufficient intensity and wavelength to kill cells in the passing air. 
     As provided above, system  700  may additionally include a fluid pump  703 . Fluid pump  703  may be any type of blowing apparatus such as a fan or pump. Fluid pump  703  preferably provides sufficient airflow volume to effectively remove moisture from the material to be dried, and sufficient pressure to pass the air through the chambers  702 ,  705 ,  707 , including the sterilization chamber  707  back-pressure if present. In some embodiments, fluid pump  703  includes multiple fans or blowers. For example, dehumidifying chamber  702  may include a built-in fan to urge air into the drying chamber  705 , and another fan may be positioned between the drying chamber  705  to urge air into the sterilization chamber  707  and a third fan may be arranged to draw air out of the sterilization chamber  707  and pass the air through a filter before release. 
     The system  700  may be open-cycle or closed-cycle. An open-cycle system draws air from the environment or other source such as a compressed-gas cylinder, dehumidifies it if necessary, passes it over the material to be dried, sterilizes it, and then releases it to the environment. A closed-cycle system passes the air from the sterilization chamber  707  back to the dehumidifying chamber  702  for re-use. The open-cycle system is simpler, but the closed-cycle system may be more economical when using an alternative gas such as nitrogen for drying. 
     In an exemplary embodiment, to remove water from the wet biomass, the biomass is spread in a thin layer across the screens  706 . Perforations in the screens allow the air or dry gas access to both upper and lower surfaces of the biomass layer. The chamber  705  is then closed. 
     An air dehumidifier or cylinder of compressed dry gas (e.g., nitrogen or helium—any gas that is inert with respect to biological materials) is connected to a fan or pump  703  to force it through the drying chamber  705 , largely parallel to the layers. The fan or pump  703  may be connected at the inlet, forcing the air through; or it may be connected at the outlet, using a vacuum to draw the air through; or both. The dry gas or dehumidified air flowing past the layer effectively draws water from the biomass. 
     During this process, the gas may pick up microscopic amounts of biological material, including cells of the microbial culture, as it passes through the drying chamber  705 . To prevent spreading of potentially undesirable organisms, in one embodiment, the air is bubbled through a reservoir of bleach or other biocidal liquid upon exiting the drying chamber  705  in sterilization chamber  707  before being released into the atmosphere. Alternatively, the air may pass through a region of intense ultraviolet illumination that also acts as a biocide. This alternative embodiment is shown in  FIG. 8 , described below. 
     Referring now to  FIG. 8 , in an alternate embodiment, system  800  includes a dehumidifying chamber  801 , a drying chamber  803 , and a sterilization chamber  807 . System  800  may additionally include hoses or connectors  802 . Drying chamber  803  may include one or more perforated drying screens or perforated shelves  805  for drying material to be dried  804 . Sterilization chamber  807  may include an ultraviolet lamp  808  that emits ultraviolet radiation  809 , which is used to sterilize the air. System  800  may additionally include a fan  811  having blades  811   a  and filter  812 . Once again, arrows indicate air flow. 
     As provided above, a system or apparatus for removing moisture from biological material includes: a source of low-humidity air or dry inert gas, a first enclosure containing material to be dried (e.g., drying chamber), a second enclosure containing means for sterilizing matter (e.g., sterilization chamber), means for moving the air through the first enclosure so as to evaporatively dry the material to be dried, and means for moving the air from the first enclosure through the second enclosure so as to sterilize the air prior to release. 
     Benefits of the system for drying the biomass include:
         No exposure to elevated temperatures, preserving stability of heat-sensitive chemicals of interest;   Rapid drying due to thin-layer distribution of the biomass, exposure to dehumidified air or dry gas, and reliance on continuous air flow;   Reduced energy expenditure by avoiding either heating or active cooling of materials; and   Active control of the exhaust gas to prevent the spread of undesirable organisms.       

     Because extracted liquids may contain residual nutrients, as well as microbial cells that escaped harvest, this fluid may be recycled. For example, in one embodiment, the recycled fluid constitutes a portion of the starting broth (e.g., liquid medium) of the next production cycle. Because the fluid may also contain metabolites released by the reproducing and digesting microbes, and high metabolite concentration may inhibit the succeeding production cycle, in one embodiment, the recycled fluid is treated to neutralize the metabolites. The recycled fluid may also, in some instances, be sterilized. 
     Following collection, the cellular biomass is exposed to a cell disruptor, e.g., means for extracting the lipid material from within the cells. In some embodiments, the cell disruptor frees lipids from microbe cells using, for example, heat, cold, ultrasound or chemical disruption (lysis) of the cells. In one embodiment, chemical lysis includes utilizing a chloroform-methanol solution to lyse the cells and their internal structures. Without wishing to be bound by any particular theory, it is believed that the methanol disrupts the cell, and the chloroform extracts the lipids. Other chemical solvents, including but not limited to methylene chloride and chloroform-methanol, as well as hexane-ethanol and others, may also be used in chemical lysis and lipid extraction. 
     Once the lipids have been released from the intracellular structure, they are separated from the cellular debris. In some embodiments, a mechanical lipid separator is used. For example, a doctor-blade to guide a floating lipid-rich mass from the top of the mixture, a sump to draw heavier components from the bottom of the lipid separator, or other port means depending on the properties of the lipids may be used. Furthermore, in some embodiments, a chemical solvation process may be utilized to provide a higher level of purity of TAG. For example, using light alkane solvents like hexane or heptanes yields a purer TAG than mechanical means because phospholipids and proteins are insoluble in alkanes. Consequently, the resulting TAG may be low in contamination by phosphorus and metals, which is desirable in some fuels. 
     After extraction of TAG, TAG is converted into hydrocarbons that may then be fractionated to form constituents of gasoline, diesel or jet fuel. Such conversion process is known to those skilled in the art. TAG can also be converted into alkyl esters such as methyl or ethyl to form biodiesel, via transesterification, in conversion process known to those skilled in the art. 
     Referring now to  FIG. 9 , a flow chart of a microbial biomass or intermediary product collection process  900  in accordance with an embodiment of the invention is shown. The microbial collection process  900  includes a receiving stage  910  for receiving the depleted fluid  540  with suspended microbes containing TAG from the inoculation and fermentation process  500  and uses one or more separation technique as described herein to harvest or collect  920  microbial biomass or intermediary product  930 . In some embodiments, mechanical means such as one or more of filtration, sieving, screening, centrifugation or precipitation, is used to separate the microbial biomass  930  from the depleted liquid  925 . 
     In some embodiments, the depleted liquid  925  is recycled as part of the water  134  added to the feedstock in the pretreatment stage  100  of  FIG. 1 . The depleted liquid  925  may require buffering, not shown, to mitigate the otherwise inhibitory effect of metabolites secreted by the microbes in the metabolization stage  530  of  FIG. 5 . 
     The microbial biomass or intermediary product  930  consists of wet microbial biomass. Accordingly, a drying step  940  may optionally be performed, to speed the extraction process. The drying step  940  may utilize heating in an oven, heating and evacuation in a vacuum oven, lyophilization, with or without use of a cryogenic liquid, or other desiccation means. The result of this step  940  is a dry cellular biomass or intermediary product  950 . 
     Either the wet biomass  930  or the dry biomass  950  is then subjected to a cell disruption step  960  that breaks up the cell structures to render the TAG accessible to chemical solvents. The cell disruption step  960  may utilize methods including one or more of mechanical, thermal, or chemical methods. For example, mechanical disruption methods may include one or more of ultrasonic, cutting, pressing, rolling or abrading means. Thermal methods may use heated air or microwave energy, among other means. Chemical means use one of several chemical agents, including but not limited to chloroform, chloroform and methanol, or methylene chloride. The output of the cell disruption step  960  is a biomass with liberated TAG  970 . Disrupting chemicals used in this step  960  may be captured, recovered and reused in a closed-cycle system. The microbial collection process  900  also includes a TAG extraction or initial purification step  980 . In some embodiments, TAG extraction is performed via chemical solvation, using solvents including short-chain alkanes such as hexane and heptanes. Solvation is followed by decantation, repeated as needed to achieve the required purity of TAG and freedom from contaminants. The output of the TAG extraction step  980  is extracted and purified TAG  984 , along with cellular debris  988 . Solvents used in this step  980  may be captured, recovered and reused in a closed-cycle system. 
     As stated above, the dry biomass contains the TAG within the microbial cells. The next step simultaneously disrupts the cell and extracts the TAG. In one embodiment, it relies on a mixture of solvents:
         a. a polar organic solvent or alcohol-based solvent (such as methanol, ethanol, isopropanol, or the like) to disrupt the cell structures and also extract the lipids, and   b. a non-non-polar organic solvent (such as hexane, heptanes, chloroform, methylene chloride, or the like) to extract the lipids efficiently.       

     In one embodiment, the solvent comprises a mixture of 10% methanol and 90% chloroform, by volume. In another embodiment, the solvent comprises a mixture of 10% ethanol and 90% hexane. Generally, the amount of methanol used can vary between 0% and 30% and the amount of ethanol used can vary between 0% and 30%. The nonpolar organic solvent completes the balance (e.g, so that the solvent mixture adds to 100%). The percentages need not be precise. 
     If the dry biomass is dense and jerky-like, it may be pre-soaked in the solvent mixture for several hours prior to the next step. If it is porous and fluffy, pre-soaking is not needed. 
     Cell disruption and TAG extraction proceeds by percolating hot solvent mixtures repeatedly through an amount of dry biomass. In the laboratory, this can be accomplished by a Soxhlet apparatus. At an industrial scale, the Soxhlet apparatus may be replaced by a system that is more robust and more energy-efficient at large scale. The underlying chemical principle remains the same: repeated exposure of the dry biomass to the hot pure solvents until nearly all the cells are disrupted and nearly all the liquids including neutral lipid TAG has escaped the biomass and gone into solution. In the Soxhlet apparatus, heat is applied to a reservoir of solvent, causing it to boil. The vapor rises until it condenses in a condenser cooled just below the boiling point. The condensate drips into a vessel containing the dry biomass (e.g., inside a filter). The hot, pure (and hence chemically more active) solvent level rises to submerge the biomass. In the Soxhlet process, the solvent is not only hot, but pure, because it is recondensed from vapor. Consequently, as more material is dissolved and extracted from the biomass, the material is collected in the reservoir and the solvent is boiled off, making it pure when is comes into contact with the biomass. 
     A siphon at the top of the vessel completely drains the vessel back into the solvent reservoir every time the liquid in the vessel reaches the top of the bend in the siphon. The biomass, constrained inside the filter, cannot flow with the draining fluid, so that the reservoir only collects fluid. This process can take several tens of minutes. During this time, the solvent mixture is both breaking down the cell structures and dissolving the TAG (and other intracellular molecules). When the vessel empties into the solvent reservoir, it now carries the solute with it. The cycle of evaporation-condensation-filling-dissolving-siphoning may be repeated until no further significant quantity of TAG is extracted from the biomass. 
     In some embodiments, the reservoir contains lipids (e.g., TAG), other biomolecules soluble in the polar solvent, and the solvent itself. An evaporation and distillation stage evaporates the solvent out of the mixture and condenses it, recapturing the solvent for reuse. What now remains in the reservoir is called crude TAG, since it may contain impurities. 
     A refining step includes treating the crude TAG in a solvent made of short-chain hydrocarbons such as heptane or mixtures of heptane with hexane or petroleum ether. One embodiment uses a 1:1 mixture of heptane and low-boiling-point petroleum ether (with boiling point between 40° C. and 60° C.). 
     This organic mixture is then decanted off or centrifuged from the insoluble residues and the organic layer is washed with brine (NaCl in water) or other alkali salt solution. TAG remains dissolved in this solvent, while phospholipids, methanol, proteins and other impurities soluble in water are washed out. While not wishing to be bound by any particular theory, it is generally important to remove phospholipids, as many transport fuel specifications require low levels of phosphorus in the fuel. 
     In one embodiment, the brine wash is followed by a deionized water wash, which removes the NaCl. Following the water wash, the material may be dried using anhydrous sodium sulfate (Na 2 SO 4 ) to remove residual water. Other analogous materials can also be used for the drying step. The sodium sulfate is thereafter removed by filtration (e.g., using filter paper in a sintered-glass filter funnel). The filtered liquid containing the extracted TAG is heated to evaporate the petroleum solvents (e.g., heptane and petroleum ether), which may be re-condensed for reuse. This process produces the purified TAG as an oily residue. 
     In an exemplary embodiment, approximately 2 kg of wet biomass yields ≦1 kg of dry biomass. As an example, approximately 6 L of nonpolar-polar solvent mixture is used in the Soxhlet to extract the TAG. The approximately 6.1 L of TAG-solvent mixture is evaporated to yield approximately ≦0.1 L of TAG. Approximately 100 mL of heptane-petroleum ether solvent and similar quantities of brine and deionized water, and approximately 50 gm of sodium sulfate, anhydrous, are used to purify the TAG, yielding ≦0.1 L of final product. As can easily be appreciated, the above numbers do not represent the best possible TAG yield, but are merely examples of amounts that can be expected in a moderate-scale laboratory implementation of the process. 
     In accordance with some embodiments, a method of producing TAG includes a number of steps, each of which are shown in  FIG. 10A . In one embodiment, a TAG extraction and purification process  1000  includes: starting with wet biomass in step  1005 , optionally drying the biomass (not shown), optionally pre-soaking the dry biomass in a mixture of nonpolar and polar organic solvents in step  1010 , disrupting the cell structures and extracting the TAG in step  1015  (e.g., via a Soxhlet-like process using a mixture of alcoholic and non-polar organic solvents), evaporating the solvent mixture from the collected liquid to produce crude TAG in step  1020 , mixing the crude TAG with a light-hydrocarbon solvent in step  1025 ; decanting the organic layer off from the insoluble residue in step  1030 , washing the resulting mixture (organic layer) with brine or other alkali salt solution and removing the water-soluble impurities in step  1035 , washing the resulting liquid in water to remove the salt in step  1040 , removing water from the resulting liquid using sodium sulfate, anhydrous, or other suitable material in step  1045 ; filtering the resulting liquid (e.g., using filter paper and a sintered-glass filter funnel) in step  1050 ; and evaporating the light-hydrocarbon solvents from the resulting liquid in step  1055 , resulting in purified TAG in step  1060 . 
     Referring now to  FIG. 10B , a method of producing TAG, in accordance with another embodiment, is shown. With the appropriate choice of microbe and culture nutrients, the crude TAG produced by the extraction process (using, for example, the ethanol-hexane solvent mixture) includes approximately 10% phospholipids, approximately 5% free fatty acids, and the remainder mostly TAG, with some mono-acyl-glycerides and di-acyl-glycerides. Purification of the crude TAG removes phospholipids and free fatty acids, to the extent specified by downstream processes that upgrade TAG into fuel. 
     Similar to the method shown in  FIG. 10A , TAG extraction and purification process  1400  includes: starting with wet biomass in step  1405 , optionally drying the biomass (not shown), optionally pre-soaking the dry biomass in a mixture of nonpolar and polar organic solvents in step  1410 , disrupting the cell structures and extracting the TAG in step  1415  (e.g., via a Soxhlet-like process using a mixture of alcoholic and non-polar organic solvents), evaporating the solvent mixture from the collected liquid to produce crude TAG in step  1420 . 
     Crude TAG is combined with a chosen acid in step  1425 . Typically, phosphoric acid of 85% concentration is used (a concentration that is conveniently available from suppliers), and this material is added in a volume ratio of approximately 1:100, acid to crude TAG. The ratio may vary by a factor of five in either direction. A citric acid solution of approximately 10% can be used as an alternative to phosphoric acid. The phospholipids and acid form a salt that separates from the TAG in step  1430 . After mixing the acid and crude TAG, the material is centrifuged in step  1435  to enable removal of the bulk of the phospholipid salts. 
     Centrifugation is followed by a wash of the TAG with pure water in step  1440 , further separating impurities that are removed by another centrifugation. This water wash and centrifugation step may be repeated, if needed, as shown in step  1445 . 
     The TAG at this point (step  1450 ) is believed to contain up to approximately 5% or more free fatty acids. Some downstream processes can make use of these acids and convert them to fuel, while others cannot. If the downstream process can use the free fatty acids, then the TAG is deemed sufficiently purified and is delivered for conversion to fuel in step  1455 . If not, the following additional purification steps are performed. 
     A titration is performed on an aliquot of the TAG to quantify its free fatty acid concentration in step  1465 . Using a procedure well known in the art, the appropriate amount of sodium hydroxide is calculated, and that amount is added to the TAG in step  1460 . The sodium hydroxide combines with the free fatty acids, yielding soap (the process is called saponification) in step  1465 . The soap is removed via a centrifugation step, as shown in step  1470 . 
     Centrifugation is followed by a wash of the TAG with pure water in step  1475 , further separating impurities that are removed by another centrifugation in step  1480 . This water wash and centrifugation step may be repeated, if needed. The end result of this process is purified TAG delivered for downstream conversion to fuel (shown in step  1485 ). 
     Referring now to  FIG. 11 , a biomass drying process  1100  is shown. Drying process  1100  includes optional paths for no drying  1110  (resulting in untreated wet biomass  1115 ), for mechanical removal of gross water only  1120  (resulting in partially dried biomass  1125 ), for mechanical water removal followed by more thorough drying  1130  (resulting in dry biomass  1135 ), and for thorough drying not preceded by mechanical water removal  1140  (resulting in dry biomass  1135 ). Three means for thorough drying are shown: lyophilizing  1150 , using a vacuum oven  1170 , and other drying means  1160  (e.g., drying apparatus shown in  FIGS. 7 and 8 ). 
     In some embodiments, maintaining the purity of the solvent, as is done by the evaporation-recondensation cycle in the Soxhlet apparatus, is not, in fact, necessary to obtain efficient extraction of the lipids. As is easily appreciated, in the Soxhlet, the biomass remains stationary inside a confining filter (thimble), and the solvent acts by diffusive processes within the biomass. In such a diffusion-dominated extraction, it is important to keep the chemical kinetics favorable to continued dissolution of the lipids in the solvent. If the solvent were allowed to accumulate dissolved lipids, the chemical kinetics of dissolution would become less favorable due to partition coefficients of the lipids in the solvents, leading to limited efficiency of lipid extraction. 
     In an alternative embodiment, the biomass is not confined to be stationary inside a filter (e.g., such as in the Soxhlet apparatus), but is freely suspended, as a slurry, in the solvent. An agitator such as, for example, a rotary stirring mechanism moves the biomass in a solvent bath. In some embodiments, the solvent is heated to a temperature range typically between about 50 and 100° C., or in general from about half the boiling point of the solvent mixture up to just below the boiling point of the solvent mixture. 
     Physical agitation ensures that the solvent reaches all portions of the biomass. Generally, agitation makes the chemical kinetics of dissolution more favorable, so that extraction effectiveness may be achieved that is equivalent to the Soxhlet process. In effect, physical agitation replaces the evaporation-condensation cycle; in both cases, the solvent is heated to increase the kinetics of the dissolution reaction. While not wishing to be bound by any particular theory, it is believed that by avoiding the two phase transition cycle required in the Soxhlet process, the heating-physical agitation method saves a very significant amount of energy and cost. For example, evaporation and condensation is needed only at the final separation stage, and then only needs to be performed once instead of many times over. While not wishing to be bound by any particular theory, it is also believed that the physical apparatus required for this physical agitation-based process is much less expensive than that required for the Soxhlet process, thus saving a significant amount of capital expenditure. 
     Following the dissolution process, the lipid-laden solvent is separated from the biomass via physical filtration. An evaporation stage evaporates the solvent; thus, the solvent is recaptured in its pure state to process the next batch of biomass and leaves the crude lipid extract to be processed further. 
     In some embodiments, the cellular debris  988  is sent to a gasifier and consumed to produce on-site electricity and/or process heat. The cellular debris  988  may also be used as part of the carbon and non-carbon nutrients in the metabolization stage  530  of  FIG. 5 . Alternatively, the cellular debris  988  may be collected, processed and sold as other products, such as livestock feed. 
     As is easily appreciated, TAG produced in accordance with embodiments of the present invention may be used as a liquid fuel suitable for transportation uses. In some embodiments, the fuel product includes saturated non-aromatic hydrocarbon molecules (e.g., alkanes and branched alkanes) with molecular weights in a predetermined range (e.g., as required by vehicle engines). 
     Table 1 shows exemplary TAG produced by a selected strain of microbes. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Produced TAG 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Glucose/ 
               
               
                   
                 Name 
                 Double 
                 Glycerol 
                 Glycerol 
               
            
           
           
               
               
               
               
               
               
            
               
                 Name 
                 length 
                 bonds 
                 Sample A9 
                 Sample A12 
                 Sample A9 
               
               
                   
               
               
                 Palmitic 
                 16 
                 0 
                 22.57% 
                 21.57% 
                 19.30% 
               
               
                 Stearic 
                 18 
                 0 
                 13.55% 
                 16.72% 
                 13.60% 
               
               
                 Oleic 
                 18 
                 1 
                 27.70% 
                 28.51% 
                 45.10% 
               
               
                 Linoleic 
                 18 
                 2 
                 30.32% 
                 26.90% 
                 17.60% 
               
               
                   
                 TOTAL 
                   
                 94.14% 
                 93.70% 
                 95.60% 
               
               
                   
               
            
           
         
       
     
     As shown in Table 1, the microbes were provided either glycerol or a combination of glucose and glycerol as their carbon source. The main components of this particular TAG product include linoleic acid, oleic acid, stearic acid and palmitic acid. The carbon chain length distribution in Table 1 indicates that any liquid transportation fuel can be refined from the product, with reasonable efficiency. In addition to the major components identified in the Table 1, the TAG includes 1-2% lignoceric acid (24-carbon chains, 0 double bonds), and less than 1% each of fatty acids with carbon chain length X and number of double bonds Y, indicated as (X:Y), as follows: (14:0), (15:0), (16:1), (17:0), (18:3), (20:1), (20:2), (20:4), (22:0). 
     As is easily appreciated, the product composition may be adjusted, by varying process conditions, to partially offset feedstock variations and to meet application specifications. Depending on product specifications, in some embodiments, the liquid fuel product may contain a proportion of saturated aromatic carbon compounds. For example, jet fuel specifications call for aromatic components comprising between 8% and 25%, by weight, of the total fuel composition. 
     Extracting Aromatic Compounds 
     As stated above, extracting product from a digester is different, depending on whether the product is TAG from cellulose breakdown or aromatic hydrocarbons from lignin breakdown. The digester that receives the solid, lignin-rich portion of pretreated feedstock includes water, nutrients and an appropriate inoculum added to break the lignin down into a variety of aromatic compounds. At the end of the fermentation or digestion cycle, the solid mass is a combination of microbes and undigested solid feedstock. 
     The aromatic compounds are included as part of the liquid and gas phase of the digester output (rather than being stored intracellularly as in TAG production). This is because the microbes break lignin down not primarily to digest it for nutrient value, but to gain access to proteins inside the lignin structures. Thus, the microbes do not absorb and metabolize the lignin breakdown products. 
     In some embodiments, the solid portion of the digester contents is largely waste that can be disposed of or gasified to produce electricity and process heat. Standard chemical separation and purification processes may be implemented to capture the aromatics from the liquid and gas-phase outputs of the fermentation. 
     After extraction of the aromatic compounds, the aromatics may then be fractionated by molecular weight. The fractionated aromatics may then be blended with alkanes to form constituents of gasoline, diesel or jet fuel. Such blending process is known to those skilled in the art. 
     Referring now to  FIG. 12 , a flow chart of a separation process  1200  in accordance with an embodiment of the invention is shown. The separation process  1200  includes a receiving stage  1210  for receiving the mixture  640  containing depleted solids, microbes, and gas and liquid containing the desired aromatic compounds yielded by the metabolization step  630  of  FIG. 6 . 
     The separation process  1200  subjects the mixture  640  to a mechanical solids separation step  1220 . This separation step  1220  uses one or more of standard mechanical means such as screening, sieving, centrifugation or filtration to achieve the separation. The separated depleted solids and microbes  1225  can be sent to a gasifier and consumed to produce on-site electricity and/or process heat. Alternatively, the depleted solids may be collected, processed and sold as other products, such as livestock feed. In yet another embodiment, the separated depleted solids and microbes  1225  may be further processed, such as via lipid extraction  1250 . 
     The separation step  1220  also outputs liquid and gas  1230  containing the target aromatic compounds. A chemical separation step  1240 , using standard chemical processes known in the art, separates aromatic compounds from the others and fractionates them by molecular weight, yielding the aromatic compounds of interest  1244 . The byproduct of this chemical separation step  1240  is the waste gas and liquid  1248 , which may contain microbial cell bodies. In some embodiments, this waste liquid  1248  is recycled to form part of the input water mixture  134  of the feedstock pretreatment stage  130  of  FIG. 1 . 
     The production of TAG and aromatic compounds may be associated with or implemented by a cellulose processing plant and/or a bio-refinery producing transportation fuel. The association may be integral, parallel, or separate. 
     In some embodiments, a cellulose processing plant receives agricultural waste (or other cellulosic material), converts it into TAGs by microbial action, and then extracts intermediates from TAGs that may be converted to fuel. In contrast, a bio-refinery typically receives TAG and aromatic compounds, processes them and blends them into transportation fuels. 
     In one embodiment, the production of TAG and aromatic compounds is implemented by a cellulose processing plant in parallel with a bio-refinery. In such an embodiment, glycerol produced by the bio-refinery is used to generate further lipids, and then either convert the lipids into fuel or pass the lipids to the bio-refinery plant which converts the lipids to fuel. 
     In another embodiment, the production of TAG and aromatic compounds is implemented by a cellulose processing plant integrated with a bio-refinery. In such an embodiment, the cellulose processing system is utilized to produce glycerol. For example, the same vessel may contain both the cellulose digestion mixture and the glycerol consumption mixture intermingled. The microbes for cellulose digestion and glycerol consumption may be intermingled if they are compatible. It is envisioned that the same microbe may perform both cellulose digestion and glycerol production simultaneously. Similarly, a single combined lipid product may be recovered from both processes. 
     In another embodiment, the production of TAG and aromatic compounds is implemented by a cellulose processing plant separate from a bio-refinery. In such an embodiment, the glycerol processing is separate from the cellulose processing. In one example, the glycerol feed may be reduced all the way to the fuel product. Alternatively, the glycerol feed may provide lipids as an intermediate product, with fuel production being completed at the separate bio-refinery or chemical refinery. In some embodiments, alkanes are extracted from TAGs and recycled in the glycerol processor to generate further fuel. This process may be repeated in cyclical fashion until the feed material is exhausted. 
     From the above description, a method in accordance with embodiments of the present invention, include a series of steps. These steps include one or more of the following:
         (1) Receiving and pretreating cellulosic feedstock;   (2) Optionally, adding glycerol obtained as a co-product of TAG transesterification;   (3) Separating the pretreated feedstock into liquid and solid phases;   (4) Inoculating the liquid phase with microbes that are capable of converting the carbon into lipids, then allowing the microbes to do so;   (5) Harvesting the resulting microbial biomass from the liquid;   (6) Extracting the lipids for subsequent conversion into fuels.   (7) Mixing the solid-phase pretreated feedstock with water and nutrients, then inoculating it with microbes capable of attacking the lignin and converting it into aromatic compounds;   (8) Separating the resulting aromatics from the liquid and gas phases of the digester output;   (9) Recycling the remaining solid-phase matter as a co-product or as feed for gasification and conversion to heat and electricity or as added carbon feedstock for subsequent microbial processing;   (10) Recycling the liquid-phase matter as broth for the next batch of feedstock and fermentation.       

     Additionally, in some embodiments, the pretreatment process  100 , as shown in  FIG. 1 , leaves considerable cellulose and hemicellulose in the solid phase or portion  148 . In such embodiments, the solid-phase feedstock  148  is inoculated with a consortium of microbes that includes species to digest the cellulose and hemicellulose and produce intracellular TAG as well as species to break down the lignin and secrete aromatic molecules in step  620 . Following the metabolization step  630 , the aromatic compound separation  1220  proceeds as indicated in  FIG. 12 , but the solid phase extract  1225  is no longer mere waste or recycling material, but is subjected to the TAG extraction process  980  of  FIG. 9 . 
     In some embodiments, the liquid-solid separation step  140  at the end of the feedstock pretreatment process  100  of  FIG. 1  is absent. In such embodiments, the unseparated feedstock is inoculated with a consortium of microbes capable of digesting both liquid and solid phases, the aromatic compounds are separated as shown in  FIG. 12 , and the TAG is extracted as shown in  FIG. 9 . 
     Turning now to  FIG. 13 , a system  1300  for producing TAG in accordance with an embodiment is shown. System  1300  includes a processing plant or facility  1310  in communication with a controller  1390 . In one embodiment, processing plant  1310  communicates with controller  1390  via a network connection  1380 . Network connection  1380  may be wireless or hard-wired. Network connection  1380  may also include the use of a web browser or other internet connectivity to allow observation and control from a remote location. 
     In some embodiments, controller  1390  provides operating instructions for processing plant  1310 &#39;s operating conditions. Controller  1390  may receive information from processing plant  1310  and utilize the information as feedback to adjust operating instructions to processing plant  1310 . Parameters that can be actively controlled in this way include, among others, temperature, pH, dissolved oxygen, and the controlled continuous feed or carbon and/or carbon nutrients. 
     In one embodiment, the operating conditions may be presented on a monitor or display  1395  and a user may interact with the operating conditions via a user interface. The monitor  1395  may be in the form of a cathode ray tube, a flat panel screen or any other display module. The user interface may include a keyboard, mouse, joystick, write pen or other device such as a microphone, video camera or other user input device. 
     Processing facility  1310  includes sterilization process equipment or sterilizer  1320 , solids extraction process equipment or solids extractor  1330 , bioreactor  1340  (e.g., fermentation process equipment or fermentor), microbial biomass extraction process equipment or microbial biomass extractor  1350 , cell disruption process equipment or cell disruptor  1360  and TAG extraction and purification process equipment or TAG extractor  1370 . In one embodiment, cell disrupter  1360  is microbial biomass process equipment. In some embodiments, controller  1390  is in communication with fermentor  1340  and provides/controls the operating conditions of fermentor  1340 . 
     Sterilization process equipment  1320  and solids extraction process equipment  1330  together perform the cellulosic feedstock pretreatment process  100  of  FIG. 1 . Fermentation process equipment  1340  performs the inoculation and fermentation process  500  of  FIG. 5 . Microbial biomass extraction process equipment  1350 , cell disruption process equipment  1360  and TAG extraction process equipment  1370  together perform the microbial biomass collection process  900  of  FIG. 9 . 
     Those of skill will appreciate that the various illustrative logical blocks, modules, and algorithm steps described in connection with the embodiments disclosed herein can often be implemented as electronic hardware, computer software, or combinations of both. To clearly illustrate this interchangeability of hardware and software, various illustrative components, blocks, modules, and steps have been described above generally in terms of their functionality. Whether such functionality is implemented as hardware or software depends upon the design constraints imposed on the overall system. Skilled persons can implement the described functionality in varying ways for each particular application, but such implementation decisions should not be interpreted as causing a departure from the scope of the invention. In addition, the grouping of functions within a module, block or step is for ease of description. Specific functions or steps can be moved from one module or block without departing from the invention. 
     The various illustrative logical blocks and modules described in connection with the embodiments disclosed herein can be implemented or performed with a general purpose processor, a digital signal processor (DSP), application specific integrated circuit (ASIC), a field programmable gate array (FPGA) or other programmable logic device, discrete gate or transistor logic, discrete hardware components, or any combination thereof designed to perform the functions described herein. A general-purpose processor can be a microprocessor, but in the alternative, the processor can be any processor, controller, microcontroller, or state machine. A processor can also be implemented as a combination of computing devices, for example, a combination of a DSP and a microprocessor, a plurality of microprocessors, one or more microprocessors in conjunction with a DSP core, or any other such configuration. 
     The steps of a method or algorithm described in connection with the embodiments disclosed herein can be embodied directly in hardware, in a software module executed by a processor, or in a combination of the two. A software module can reside in RAM memory, flash memory, ROM memory, EPROM memory, EEPROM memory, registers, hard disk, a removable disk, a CD-ROM, or any other form of storage medium. An exemplary storage medium can be coupled to the processor such that the processor can read information from, and write information to, the storage medium. In the alternative, the storage medium can be integral to the processor. The processor and the storage medium can reside in an ASIC. 
     The above description of the disclosed embodiments is provided to enable any person skilled in the art to make or use the invention. Various modifications to these embodiments will be readily apparent to those skilled in the art, and the generic principles described herein can be applied to other embodiments without departing from the spirit or scope of the invention. For example, while the feedstock received by a cellulose processing plant has been referred to as containing cellulosic material, any type of feedstock which may yield alkanes and/or aromatic compounds may be used. Thus, it is to be understood that the description and drawings presented herein represent a presently preferred embodiment of the invention and are therefore representative of the subject matter which is broadly contemplated by the present invention. It is further understood that the scope of the present invention fully encompasses other embodiments that may become obvious to those skilled in the art and that the scope of the present invention is accordingly limited by nothing other than the appended claims.