Biochemical Sources of Fuels

By John D. Keenan, Assistant Professor of Civil and Urban Engineering, University of Pennsylvania, Philadelphia, Pa.

From Considine, Douglas M. (Ed-in-Ch): Energy Technology Handbook (McGraw-Hill, 1977)

FUELS considered here are those elaborated by or otherwise rendered available by living systems. The discussion is limited to a short geological time scale, thus eliminating the fossil fuels from direct consideration. Fossil fuels are described in considerable detail in earlier portions of this Handbook.

Energy and carbon are obtained by organisms either directly or indirectly via the photosynthetic conversion of solar energy. These organisms have evolved metabolic machineries for the photochemical reduction of carbon dioxide to organic matter and/or for the subsequent utilization of the organics for biosynthesis and controlled energy Iiberation. These metabolic routes can be exploited to provide fuels from biochemical sources.

The majority of the bioengineering strategies for biochemically derived fuels involve options for the disposition of organic matter produced via photosynthate. The bulk of the presently exploited photosynthate is directed toward the production of wood, food, and feed. During processing and consumption, waste organic materials are generated which can be used for energy production via combustion, pyrolysis or biochemical conversions to ethanol, hydrogen, methane, and isopropanol. A second option is to engineer the photosynthetic apparatus to provide hydrogen. The third strategy is the cultivation of crops as energy sources, i.e., the farming of an energy crop which can be used as an energy source via the foregoing processes.

The discussion here follows this general outline -- photosynthesis to organic matter, photosynthesis to hydrogen, and biochemical conversion of organic matter to fuels. Several other topics are discussed briefly, including the microbiological extraction of shale oil, conversion economics, and the application of biochemical engineering principles to fuel generation. Cross references at the end of this discussion are given to other areas of this Handbook where some of these topics are covered in even greater detail.


The photosynthetic apparatus and the mechanisms by which it operates have been intensively investigated over the past 30 to 40 years. The current understanding (Ref. 1) is that of three series of interconnected oxidation-reduction reactions: The first involves the evolution of oxygen from water. The second is the transfer of H atoms to a primary hydrogen acceptor. The third is the reduction of CO2 to carbohydrates by the primary hydrogen acceptor. The light energy required for photosynthesis is used to drive the H atoms against the potential gradient.

The photochemical stage of photosynthesis consists of two separate steps, I and II. The products of light reaction II are an intermediate oxidant and a strong oxidant which is capable of oxidizing water to oxygen. An intermediate oxidant and a strong reductant that can reduce carbon dioxide are produced in light reaction I. The two light reactions involve two pigment systems, photosystems I and II, interconnected by enzymatic reactions coupled with photophosphorylation yielding adenosine triphosphate (ATP) . ATP is one of several high energy (7 to 8 kcal liberated upon hydrolysis per mole) compounds used in biological systems for chemical energy storage.

Plant Cultivation

Agricultural productivities can be used to estimate photosynthetic energy conversion efficiencies. Odum (Ref. 2) summarizes net primary production rates for a number of cultivated crops. The productivities range from 344 to 6700 grams dry weight per square meter per year. Assuming the plant material to be 90 percent organic matter at 4.68 kcal per gram organic matter (Ref. 3) , and assuming incident solar radiation to be 500 cal per square centimeter per day, the photosynthetic efficiencies range from 0.07 to 1.6 percent. Energy crop production could be based on terrestrial, freshwater, or marine systems. The major problems involved are the large land areas required and the cost and energy expense of harvesting (Ref. 4).

Photosynthetic Hydrogen

Several schemes have been proposed to utilize the photosynthetic apparatus, at the cellular and molecular level, for hydrogen production. Gest (Ref. 5) has recommended the use of photosynthetic purple bacteria for the production of hydrogen. These bacteria, such as Rhodopseudomanus species, evolve hydrogen when grown in the presence of an organic carbon source. The production of hydrogen is dependent on the presence of light and an electron donor, the proper nutritional history especially with respect to nitrogen, and conditions of metabolic imbalance between energy conversion and biosynthesis.

Other proposed biosynthetic hydrogen methods involve the production of the highly reduced hydrogen carrier coupled with an hydrogenase enzyme system for removal of the H atoms as hydrogen gas. Krampitz (Ref. 5) has developed laboratory-scale reactors coupling spinach chloroplast with the hydrogenase from the bacterium Escherichia coli. Alternately, the hydrogen may be produced via photoreduction of carbon dioxide to formate followed by enzymatic conversion to hydrogen and carbon dioxide.

Among the problems involved in the application of hydrogen production via photosynthesis are maintenance of reducing conditions, land area requirements, and system management. The appropriate redox conditions can be maintained within the chloroplast environment. The oxygen sensitivity of hydrogenases may be overcome by mechanical, chemical, or enzymatic removal of oxygen, mutagenesis to yield less sensitive hydrogenases, use of hydrogenases from aerobic organisms, and use of genetic manipulation to regulate hydrogenase activity.

The areal efficiency of hydrogen generation has been estimated (Ref. 5). An optimistic production estimate is 9 moles H2 per day per square meter, corresponding to a gross energy yield of 1.92 x 10(5) kcal per year per square meter, or 1.97 x 10(12) Btu per year per square mile. The calculations assume that 25 percent of these undergo primary conversion, and that four quanta are required per hydrogen molecule. The energy conversion efficiency of this system would be on the order of 10 percent at a daily incident solar radiation of 500 cal per square centimeter.

Biochemical Oxidations

Respiration refers to those biochemical processes in which organisms oxidize organic matter and extract the stored chemical energy needed for growth and reproduction. Respiration patterns may be subdivided into two major groups, based on the nature of the ultimate election acceptor.

Although alternative pathways exist for the oxidation of various organic substrates, it is convenient to consider only the degradation of glucose. (The metabolic routes provide the means for metabolism of pentoses and for interconversions between sugars and other metabolites.) The breakdown of glucose is via the Embden-Meyerof-Parnas glycolytic pathway which yields 2 moles each of pyruvate, ATP, and reduced nicotinamide adenine dinucleotide (NAD) per mole of glucose.

Under aerobic conditions, the pyruvate is oxidized to CO2 and H2O via the tricarboxylic acid or Krebs cycle and the electron transport system. The net yield for glycolysis followed by complete oxidation is 38 moles ATP per mole glucose, although there is evidence that the yield for bacteria is 16 moles ATP per mole glucose (Ref. 6). Thus, 673 kcal are liberated per mole glucose, much of which is stored as ATP.

Under anaerobic conditions, various pathways exist for pyruvate metabolism which serve to reoxidize the reduced hydrogen carriers formed during glycolysis. The ultimate acceptor builds up as a waste product in the culture medium. The end products of the pathways are: (1) CO2, ATP, and acetate; (2) CO2 and ethanol; (3) H2 and CO2; (4) CO2 and 2,3-butylene glycol; (5) CO2, H2, acetone, ATP, and butanol; (6) succinate; and (7) lactate. The pathway that occurs depends on the microorganism cultivated and the culture.

In terms of energy liberation, the anaerobic fermentations are inherently inefficient. The end products of these metabolic activities are reduced and possess high heats of combustion. Several examples are shown in Table 1. It is the value of these products for various purposes including fuels which makes the anaerobic oxidation of organic substrates attractive.

Table 1
Heats of combustion for theoretical oxidation of glucose by various routes are shown as kcal per mole of glucose fermented
Heat of Combustion
H2O + CO2 0
2 CO2 + 2 C2H5OH 654
3 CH4 + 3 CO2 634
Mixed acid (Escherichia) 633
2 lactic acid 652
Lactic acid 654

Ethanol Fermentation

Ethyl alcohol is produced biologically by the well-known yeast fermentation (Refs. 7 to 9). Alcohol-tolerant strains of Saccharomyces cerevisiae are usually used. S. cerevisiae converts hexose sugars to ethanol and carbon dioxide, theoretically yielding 51 and 49 percent by weight, respectively. S. anamensis and Schizosaccharomyces pombe are also used. Candida pseudotropicalis is utilized for the ethanol fermentation from lactose, and C. utilis from pentoses. Ethanol can be fermented from any carbohydrate, although starchy or cellulosic materials require a pretreatment step for hydrolysis. The usable raw materials can be categorized as saccharin (sugarcane, sugar beets, molasses, and fruit juices), starchy (cereals and potatoes), or cellulosic (wood and waste sulfite liquor). Pretreatment methods are discussed elsewhere (Refs. 7 to 9).

Table 2
Heats of Combustion and Costs of Various Fuels
Cost Basis: See references cited; otherwise mid-1970s
Fuel kcal/gram* Btu/pound $/million Btu Cost references
Ethanol 327.6 12,790
Synthetic .... .... 6.54-10.70 l0-13
Fermentative 17.82-23.80 13
Hydrogen 68.4 61,500 0.89-1.02 14-15
Methane 210.8 23,600
Natural gas -- wellhead .... .... 0.20-0.25
Consumers .... .... 0.75-1.00
Anaerobic digestion .... .... 0.40-2.00
Substitute natural gas 0.52-1.50 16-19
Methanol 170.9 9,990
Natural .... .... 14.68 10
Synthetic .... .... 3.86 10
Isopropanol 474.8 14,210
Synthetic .... .... 5.18 10
*Refs. l0-11.

The environmental conditions of the alcoholic fermentation vary somewhat, depending primarily on the strain of yeast. Acidic conditions are used to inhibit bacteria1 contaminants. The initial pH is in the range of 4.0 to 5.5. Suitable temperatures are on the order of 20 to 30 deg C. Industrial alcoholic fermentations are normally operated on a batch basis, the process being completed within 50 hours. Yields are in excess of 90 percent of theoretical, based on fermentable sugars. The concentration of alcohol in the culture medium depends on the alcohol tolerance of the yeast. Typically, this is on the order of 10 to 20 percent which is increased by distillation and other techniques.

The economics of the ethanol fermentation depend on the cost associated with the carbohydrate feed material and the market for nonalcoholic by-products. These by-products consist of grain residues, recovered carbon dioxide, and the residual cells. Recovered grain and cells are normally sold as feed materials. In recent years, chemosynthesis has largely displaced fermentation for the industrial production of ethyl alcohol.

Synthetic ethanol is manufactured from ethylene by absorption in concentrated sulfuric acid followed by hydrolysis of the ethyl sulfates to ethyl alcohol, or by the direct catalytic hydration of ethylene. As of the mid-1970s, 80 percent of the ethanol synthesized in the United States is via the catalytic process (Ref. 10). The synthetic processes yield 0.25 gallon ethanol per pound of ethylene and 0.58 gallon per gallon of ethyl sulfate (Ref. 10). Mid-1970s prices for industrial ethyl alcohol are summarized in Table 2. Goldstein (Ref. 13) has estimated that for corn at $1.80 per bushel (1974 support price was $1.30 per bushel), fermentation is competitive when ethylene exceeds $0.18 per pound, approximately triple the 1974 price (Ref. 10).

Butanol-isopropanol Fermentation

The butanol-isopropanol fermentation (Refs. 7 to 9) is mediated by the anaerobic bacterium Clostridium butylicum. A wide variety of carbohydrate feeds maybe used. Saccharin feeds yield 30 to 33 percent mixed solvents, based on the original sugars. At 33 to 37 deg C. the fermentation is complete within 30 to 40 hours. Product ratios vary with the strain and with culture conditions, but are normally in the range 33 to 65 percent n-butanol, 19 to 44 percent isopropanol, 1 to 24 percent acetone, and 0 to 3 percent ethanol. This fermentation has been supplanted by petrochemical synthetic processes.

Methane Fermentation

Methane and carbon dioxide are the primary gaseous end products of the anaerobic digestion process which has been widely used for many years in the stabilization of organic sewage solids. The quality of the digester off-gases is dependent upon feed composition. Mixed feeds normally yield approximately 65 percent methane and 35 percent carbon dioxide. Approximately equal volumes arise from carbohydrates, and the methane yield increases with proteins and lipids. In addition, the product gases contain small volumes of hydrogen sulfide and nitrogen.

The generation of methane occurs as the last step of a series of biochemical reactions. The reactions are divided into three groups, each mediated by heterogeneous assemblages of microorganisms, primarily bacteria. A complex feed, consisting of high-molecular-weight bipolymers, such as carbohydrates, fats, and proteins, undergoes exocellular enzymatic hydrolysis as the first step. The hydrolytic end products are the respective monomers (or other low-molecular-weight residues), such as sugars, fatty acids, and amino acids. These low-molecular-weight residues are taken up by the bacterial cell before further metabolic digestion.

The second step is acid production in which the products of hydrolysis are metabolized to various volatile organic fatty acids. The predominant fatty acids are acetic and propionic acids. Other low-molecular-weight acids, such as formic, butyric and valeric acid, have been observed. Additional end products of the acid production step include lower alcohols and aldehydes, ammonia, hydrogen sulfide, hydrogen, and carbon dioxide.

The products of the acid generation step are metabolized by the methane-producing bacteria to yield carbon dioxide and methane, and, in addition, methane arises from metabolic reactions involving hydrogen and carbon dioxide. The current understanding of the biochemistry and kinetics of the methane fermentation is summarized in Refs. 20 and 21.

Anaerobic digestion of organic solids wastes has been investigated as an alternative methane source. Various cost estimates have been made which indicate production costs, including gas purification and compression, in the range of $0.40 to $2.00 per million Btu. The major cost items, and sources of variability in the estimates, are the digester capital costs, waste sludge disposal cost, and the credit or debit associated with the collection and preparation of the solid waste feed material. Multiple staging and separate optimization of anaerobic digestion may provide reduced capital costs through lower detention times and reduced operation and maintenance costs by improved process stability.

Hydrogen Fermentation

Hydrogen gas is a product of the mixed acid fermentation of Escherichia coli, the butylene glycol fermentation of Aerobacter, and the butyric acid fermentations of Clostridium spp. (Ref. 6) . A possible fruitful research approach would be to seek methods of improving the yield of hydrogen.

Cellulose Degradation

A significant portion of the organic matter suitable for fermentation to fuels is cellulosic. Cellulosic materials tend to resist biochemical degradation. A system has been described which utilizes fungal cellulase for the hydrolysis of cellulose (Refs. 22 and 23). Wilke (Ref. 24) described a system for the net production of 429 tons of glucose (5.88% w/w) per day from 885 tons of waste paper at a cost of $18.56 per ton of glucose, excluding credits or debits associated with the disposal of the paper.

Biochemical Fuel Cells

Young et al. (Ref. 25) have discussed the possibilities of utilizing biological processes as an integral part of fuel cells. They define three basic types of biochemical fuel cells: (1) depolarization cells in which the biological system removes an electrochemical product, such as oxygen; (2) product cells in which an electrochemically active reactant, such as hydrogen, is biologically produced; and (3) redox cells (oxidation-reduction) in which electrochemical products are converted to reactants (ferricyanide/ferrocyanide system) by the biological system. Young et al. concluded that application of biochemical fuel cells will most probably involve immobilized enzymes as a method of increasing efficiency and decreasing costs.

Extraction of Shale Oil

Several biological approaches have been suggested as adjuncts in the extraction of shale oil and subsequent processing of kerogen (Ref. 5). One procedure would utilize sulfur-oxidizing bacteria. A metabolic end product of certain sulfur oxidizers is sulfuric acid which would help to break down the inorganic matrix and thus improve the shale porosity.

An alternative strategy is the use of bacteria to partially degrade the organic kerogen phase to a more usable low-molecular-weight form. Various microorganisms capable of oxidizing hydrocarbons have been described. The general metabolic pathway is ring cleavage, if required; oxidation to fatty acid; and then degradation via the beta-oxidation route (Ref. 26). Biological methods have also been proposed for the secondary recovery of petroleum (Refs. 27 and 28). The applicability of biological processes to the development of shale oil deposits is speculative, and considerable work must be undertaken to approach the biological and engineering problems involved.

Conversion Economics

In some cases the cost of biochemical processes is fairly well understood, whereas in others very little is known. In Table 2 some mid-1970s costs are summarized for biochemical and other sources. Widespread application of these processes will be a function of competition which can occur at any of three levels. At the first level is competition for raw materials. Strong pressure will exist for utilization of photosynthate for food and feed (Ref. 29). Waste materials also face competition for alternative uses. For example, waste newsprint is $40 per ton (mid-1970s, Philadelphia area). Demand may force decisions to direct fermentation toward food and feed production instead of fuel generation. The third level of competition is alternative uses of the end product, such as synthetic feedstock and solvents.

Other factors impinging upon cost decisions are markets for by-products (feed residue, cells, carbon dioxide), land area requirements, and product extraction procedures. Cell yields are on the order of 0.119 gram per kcal taken up from the medium (Ref. 30). The biochemical fuels could relieve shortages in the petrochemical industry and would provide environmental advantages in that they generally are clean burning and renewable, and do not alter the planetary heat balance.

The biologically derived products will complement the existing energy structure. Methane gas is easily transportable in the well-developed natural gas distribution system. Ethyl and isopropyl alcohols have been utilized as gasoline additives for internal combustion engines (Ref. 31). Suggestions for widespread utilization of hydrogen fuel have been made (Ref. 32).

There are a number of other fermentations in which various metabolites accumulate which can be used to alleviate petrochemical shortages. These include acetone and n-butanol from Clostridium acetobutylicum; fats from molds; glycerol; 2-3 butylene glycol; and various acids, such as formic, lactic, citric, fumaric, and glutamic acid (Refs. 7 to 9).

It is apparent that the production of fuels by biochemical means is feasible and desirable. Process economics and efficiencies require improvement which, in turn, necessitates a concerted and coordinated research effort on the part of the biologist and the engineer. Enzyme and genetic engineering hold the key to improved process efficiencies. The immobilization of enzymes onto solid matrices has promise for increasing efficiencies by eliminating competing reactions and bringing reactants close together. Greater yields may result from the selection of better strains, alteration of genetic makeup, and taking advantage of existing enzyme regulatory mechanisms, such as enzyme inhibition, repression, and depression.

Editor's Notes

Numerous other descriptions in this Handbook touch upon several of the topics described here. In particular, further reference is suggested to Chemical Feedstocks from Natural Gas, LNG versus Methanol Route, Wood-to-Oil Process, Petro-chemical Complex, Oil Shale Processing and Fuels, Alcohol and Alcohol-Blend Fuels, Hydrogen, Batteries, Fuel Cells, Photosynthesis, Solar Physics. Consult Contents pages in front of book and alphabetical index at end of book.


1. Rabinowitch, E., and Govindjee: "Photosynthesis," Wiley, New York, 1969.

2. Odum, E.P.: "Fundamentals of Ecology," Saunders, Philadelphia, 1959.

3. Prochazka, G.J., W.J. Payne, and W.R. Mayberry: Calorific Contents of Microorganisms, Biotech. and Bioeng. 15, 1007-1010 (1973).

4. Oswald, W.J., and C.G. Golueke: Biological Transformation of Solar Energy, Advan. Appl. Microbiol., 2, 223-262 (1960).

5. Hollaender, A.K., J. Monty, R.M Pearlstein, F. Schmidt-Bleek, W.T. Snyder, and E. Volkin: "An Inquiry into Biological Energy Conversion," University of Tennessee, Knoxville, Tenn., 1972.

6. Aiba, S., A.E. Humphrey, and N.F. Millis: "Biochemical Engineering," 2d ed., Academic, New York, 1973.

7. Prescott S.C., and C.G. Dunn: "Industrial Microbiology," McGraw-Hill, New York, 1959.

8. Rhodes, A., and D.L. Fletcher: "Principles of Industrial Microbiology," Pergamon, New York, 1966.

9. Peppler, H.J.: Ethyl Alcohol, Lactic Acid, Acetone, Butyl Alcohol, and Other Microbial Products, in H.J. Peppler (ed.), "Microbial Technology," Van Nostrand Reinhold, New York, 1967.

10. "Chemical Economics Handbook," Stanford Research Institute, Menlo Park, Calif., 1974.

11. "Handbook of Chemistry and Physics," 53d ed., Chemical Rubber Co., Cleveland, 1972.

12. "Handbook of Tables for Applied Engineering Science," Chemical Rubber Co., Cleveland, 1970.

13. Goldstein, S.: "The Economics and Problems of Ethanol from Starches," presented at Symposium on the Progress of Research in Enzyme Technology and Its Application, University of Pennsylvania, Philadelphia, May 3, 1974.

14. Van den Berg, G.J., E. Reinmuth, and E. Kapp: Hydrogen from Heavy Residue, Chem. & Process Eng., 5 2 10, 49-55 (1971).

15. Anon.: Hydrogen Plants - Where They Are and Where They Are Going, Oil Gas Jl., 69, 176-182, June 21, 197l.

16. Anon.: Coal Gasification Circulates Molten Salt, Oil Gas Jl., 69, 103, Sept. 27, 1971.

17. Anon.: Synthetic Gas Processes Pushed in the U.S., Oil Gas Jl., 69, 86-87, Jan. 25, 1971.

18. Anon.: Coal Gas at 66¢/MM BTU Is Estimated by Kellogg Company, Oil Gas Jl., 70, 46, Dec. 4, 1972.

19. Finneran, J.A.: SNG - Where Will It Come from and How Much Will It Cost, Oil Gas Jl., 70, 83- 86, July 17, 1972.

20. Gould, R.F. (ed.): Anaerobic Biological Treatment Processes, in Advan. Chem. Ser., vol. 105, American Chemical Society, Washington, 1971.

21. Stadtman, T.: "Methane Fermentation," in C.E. Clifton, S. Raffel, and M.P. Starr (eds.) Ann. Rev. Microbiol., 21, 121-142. Annual Reviews, Inc., Palo Alto, Calif., 1967.

22. Mandels, M., and J. Weber: The Production of Cellulases, in R.F. Gould (ed.) Cellulases and Their Applications, in Advan. Chem. Ser., 95, 391-414, American Chemical Society, Washington, 1969.

23. Reese, E.T., M. Mandels, and A.H. Weiss: Cellulose s Novel Energy Source, in T.K. Ghose, A. Fiechter, and N. Blakebrough (eds.) Advan. Biochem. Eng., 2, 181-200, Springer-Verlag, New York, 1972.

24. Wilke, C.: "Conversion of Cellulosic Materials to Sugar and Alcohol," presented at Symposium on Progress of Research in Enzyme Technology and Its Application, University of Pennsylvania, Philadelphia, May 3, 1974.

25. Young, T.G., L. Hadjipetrou, and M.D. Lilly: Theoretical Aspects of Biochemical Fuel Cells, Biotechnol. and Bioeng., 8, 581-93 (1966).

26. Abbott, B.J., and W.E. Gledhill: The Extracellular Accumulation of Metabolic Products by Hydrocarbon-degrading Microorganisms, Advan. Appl. Microbiol., 14, 249-388, 1971.

27. Beerstecher, E., Jr.: "Petroleum Microbiology," Elsevier New York, 1954.

28. Davis, J.B.: "Petroleum Microbiology," Elsevier New York, 1967.

29. Bhattacharjee, J.K.: Microorganisms as Potential Sources of Food, Advan. Appl. Microbiol., 13, 139-161 (1970).

30. Payne, W.J.: Energy Yields and Growth of Heterotrophs, in C.E. Clifton, S. Raffel, and M.P. Starr (eds.) Ann. Rec. Microbiol., 24, 17-52, Annual Reviews, Inc., Palo Alto, Calif., 1970.

31. Pleeth, S.J.W.: Alcohol - A Fuel for Internal Combustion Engines, Chapman & Hall, Ltd., London, 1949.

32. Sailor, V.L.: "Hydrogen Economy - Based on Hydrogen as Energy Source, Brookhaven National Laboratory, Upton, NY., 1973.

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