In This Issue
Engineering, Energy, and the Future
June 1, 2003 Volume 33 Issue 2
The next industrial revolution will transform energy production and consumption

Biological Solutions to Renewable Energy

Sunday, June 1, 2003

Author: Hamilton O. Smith, Robert Friedman, and J. Craig Venter

Biological systems might be engineered to satisfy a greater part of our energy needs.

Although biological systems contribute very little to current U.S. energy requirements, they are capable of very large-scale effects. Our modern oxygen atmosphere was created 3 billion years ago by photosynthetic cyanobacteria. Our fossil fuels are derived from chemical energy accumulated over many millions of years by photosynthetic and biochemical processes that converted light energy into carbohydrates, proteins, and fats, the biological storage forms for light energy.

Today, terrestrial plants produce about 120 billion metric tons of biomass (dry weight)1 globally each year (IPCC, 2001). The energy in this biomass totals about 2,400 quads2 (1 quad = 1015 Btu). Modern economies, however, rely extensively on fossil fuels rather than biomass for their energy. In 2001, the world consumption of fossil fuels totaled about 315 quads, about one-quarter of which was consumed in the United States (BP, 2002).

Coal, natural gas, and petroleum met about 85 percent of the energy needs of the U.S. economy in 2001 (EIA, 2001).3 Unfortunately, the combustion of these fossil fuels also emitted large quantities of carbon dioxide into the atmosphere--close to 1.6 billion tons of carbon. Moreover, close to 25 quads of petroleum had to be imported. The remaining 15 percent of U.S. energy needs was met by carbon-free sources (nuclear electric power and conventional hydroelectric power) and carbon-neutral sources (biomass). Biomass energy is carbon neutral, that is, although carbon dioxide may be emitted to the atmosphere, the amount emitted is the same as the amount removed to create that biomass in the first place. Carbon-neutral biomass provides about 3 percent (3 quads) of U.S. needs, mostly from burning wood and waste; about 0.15 quads of primarily corn-derived ethanol is blended into gasoline. But the potential for biomass energy is much larger.

The question then is by how much and in what way biological systems might satisfy a greater part of our energy needs? Should we simply burn more biomass, or should we convert it to fuels, such as ethanol, methanol, hydrogen, or methane? Or is it possible to develop continuous biological processes that produce, for example, large amounts of hydrogen?

In 2002, J. Craig Venter founded the Institute for Biological Energy Alternatives (IBEA), a not-for-profit research institute located in Rockville, Maryland, to seek ways to exploit genomic knowledge and genetic engineering methods to optimize biological organisms for efficient production of alternative fuels and for carbon sequestration. IBEA is also undertaking large-scale genomic sequencing of environmental microbial populations to discover new organisms that might be of value for carbon sequestration or fuel synthesis.

Sargasso Sea Project
Only a minute fraction of the microbial organisms on earth have been examined. Many, perhaps most, of them cannot be readily grown in the laboratory. And yet, there may be some extraordinarily interesting metabolic processes in undiscovered organisms that would be extremely useful for carbon sequestration or fuel production. To explore the possibilities, IBEA is undertaking a mission to explore oceanic microorganisms. Recently, IBEA sampled and analyzed the microbial content of surface waters (down to 5 meters) at certain locations in the Sargasso Sea, a relatively defined area of the Atlantic Ocean off the coast of Bermuda. Preliminary analysis of the RNA in microbes in the size range of 0.1 to 0.8 microns reveals a few dominant organisms, plus a considerable diversity of less common species. Genomic libraries of the microbial mixtures are being sequenced to an extent sufficient to assemble the complete genomes of the most prevalent species and to sample the biochemical diversity of less common species. Once the genomic sequences are known, it may be possible to recover the genes that carry out potentially interesting metabolic processes and insert them into laboratory organisms for more detailed studies of their potential usefulness. In addition to this discovery process, IBEA plans to examine and evaluate currently known microbial organisms for applications to energy needs.

Energy-Relevant Metabolic Processes
Autotrophic organisms extract energy either from sunlight or from chemical reactions involving inorganic electron donors, such as hydrogen sulfide or iron. All other living systems either directly or indirectly use energy captured by autotrophs. Sunlight is the ultimate renewable energy source; inorganic electron donors are generally consumables. Biological processes that produce renewable energy must therefore generally use solar energy either directly or indirectly. Photosynthetic organisms use solar energy and carbon dioxide to produce carbohydrates, and the carbohydrates are used as stored chemical energy or to build biomass (proteins, fats, cellulose, etc.), which can be used directly as burnable fuel.

Fuel can also be produced by fermentation reactions that convert carbohydrates to ethanol, methane, and hydrogen. Some of the adsorbed solar energy might also be diverted directly into hydrogen production.

Fermentation Reactions
Approximately 1.7 billion gallons of ethanol are produced every year in the United States. The two-stage production process involves photosynthetic production of carbohydrate from corn and then fermentation (using yeast) of the carbohydrate into ethanol. A bushel of corn yields 2.5 gallons of ethanol, and an acre of corn yields, on average, 125 bushels; the United States plants about 70 million acres of corn. Thus the potential yield of ethanol from our entire corn crop would be 22 billion gallons, or a bit less than 20 percent of our automotive fuel needs if engines were adapted to run on pure ethanol (we use about 110 billion gallons of gasoline per year).

The overall efficiency of ethanol production from photosynthesis is low; 10 percent is often cited as a practical upper limit for the conversion of solar energy into carbohydrate by a plant. But even under the best conditions, a corn plant has about a 1 percent conversion rate of sunlight into carbohydrate. The conversion of the chemical energy in cornstarch into ethanol energy is approximately 50 percent. Thus the overall efficiency of the conversion of sunlight energy into ethanol energy is about 0.5 percent. Moreover, ethanol production is currently about break-even in terms of the energy consumed in production and the energy obtained from the ethanol.

Other fuels can be produced by fermentation of carbohydrates. For example, the anaerobic bacterium Clostridium butyricum can produce hydrogen with a theoretical yield of about 0.5 m3 of hydrogen per kg of glucose (Kataoka et al., 1997). Hydrogen could be produced in factories similar to those that now produce ethanol, and Clostridium could replace yeast. However, because not all of the hydrogen in glucose is converted to hydrogen gas, less of the chemical energy of glucose is captured in hydrogen than in ethanol.

Scientists in Germany have adopted a different, more efficient approach to producing hydrogen gas from the hydrogen in carbohydrates. They have devised a three-step bioreactor for continuous hydrogen production. In the first step, green algae produce carbohydrate by photosynthesis. In the second step, the carbohydrate is piped to a reactor of lactic acid bacteria that convert the sugar to lactic acid. Theoretically, each mole of glucose molecule is converted to two moles of lactic acid, although actual yields are somewhat lower. In the third stage, the lactic acid is routed to a fermenter containing purple bacteria where it is used as a substrate for hydrogen production. An advantage of this system is that all of the hydrogen atoms in the lactic acid can be converted to hydrogen gas by the purple bacteria
(Table 1).

Some archaeal species produce methane. For example, the acetoclastic methanogens (e.g., Methanosarcina and Methanosaeta) produce methane from acetic acid. If this reaction were coupled to the one above that yields acetic acid, the overall yield from glucose would be glucose plus water yields methane plus hydrogen and carbon dioxide, a greater yield of useful fuel. Genetic engineering might be used to transplant the methanogen pathway into Clostridium for more efficient conversion of glucose to fuel.

Direct Production of Hydrogen by Photosynthesis
Even though some of the reactions in Table 1 produce hydrogen indirectly from photosynthesis, producing and transporting the carbohydrate products of photosynthesis to the fermentation facilities where the hydrogen is produced is costly and energy consuming. It may be feasible to genetically engineer photosynthetic organisms to produce hydrogen directly.

For several decades, we have known that green algae can produce hydrogen directly from water. The enzyme hydrogenase catalyzes the reaction: hydrogen ion plus ferredoxin
-1 yields gaseous hydrogen plus ferredoxin0. Hydrogen ions and electrons are intermediates of the photosynthetic process, derived from the splitting of water, and are normally used to drive the synthesis of ATP and reduce carbon for production of carbohydrates, proteins, and fats. Normally, photosynthetic systems produce oxygen and carbohydrates but do not evolve hydrogen. However, under anaerobic conditions, hydrogenase, which is an oxygen-sensitive enzyme and is normally not expressed, becomes induced and active and catalyzes conversion of the protons and electrons to hydrogen.

Scientists at the University of California, Berkeley, have found that sulfur deprivation of Chlamydomonas reinhardtii, a green algae, turns off the normal photosynthesis pathways, causing cells to stop emitting oxygen and stop producing carbohydrate, protein, and fat energy reserves. Hydrogenase is induced and activated by the low oxygen tension, and the stored energy reserves are then used to produce hydrogen. Once the stores are depleted, sulfur must again be added to return the system to normal photosynthesis. By cycling between sulfur and non-sulfur metabolism, hydrogen can be cyclically produced in a two-stage process.

Although these studies have demonstrated the feasibility of producing hydrogen by photosynthesis, they involve either mul-tiple stages and routing of media and substrates or the intermittent evolution of hydrogen. A continuous process involving a single photosynthetic organism in which solar energy is used to split water and produce hydrogen and oxygen would be much more desirable. The cyanobacterium,
Synechocystis sp. PCC6803, would be a good choice for the photosynthetic organism because genomic information is available about the biochemical potential of this organism, and it could probably be genetically engineered more easily than eukaryotic algae or plants.

Photosynthesis is carried out by a complex but coordinated set of membrane systems. The first step, the splitting of water and resultant charge separation of a proton and an electron, is accomplished by photosystem II (PSII) using photon energy captured by chlorophyll. The electrons are used to generate a proton gradient for synthesis of ATP and then are given an additional energy boost by photons gathered in photosynthesis system I (PSI).

The net reaction of photosynthesis is: carbon dioxide plus water plus light energy yields carbohydrate plus oxygen. Normally, no hydrogenase is made, but it may be possible to manipulate the photosynthetic apparatus genetically to accentuate the hydrogenase reaction and produce hydrogen directly.

For example, under anaerobic conditions, hydrogenase could be induced and activated, and it would catalyze, in a side reaction, the formation of hydrogen from protons and ferredoxin-1. One possibility would be to alter the regulation of the chromosomal copy of the hydrogenase gene to decrease its oxygen sensitivity, thus making it active under aerobic conditions. Another possibility would be to introduce an over-expressing hydrogenase gene using an appropriate plasmid vector. The cloned gene could be from another organism that produces a hydrogenase with lower sensitivity to oxygen. The extensive library of microbial genomes could be used to search for such an enzyme. Projects such as the Sargasso Sea genome analysis may yield enzymes with desirable properties.

IBEA will also explore the feasibility of changing or broadening the light adsorption spectrum of the light-adsorbing pigments (primarily chlorophyll and phycocyanin) used by the cyanobacteria. One could possibly "graft-on" pigments from another species by cloning or directly modify the pigments by genetically engineering the pathways by which the pigments are synthesized. In general, IBEA plans to undertake detailed studies of the components of the photosynthesis apparatus and attempt to genetically engineer changes that will lead to the efficient conversion of light energy into hydrogen.

1 Carbon estimates based on 1g C ~ 2g dry weight biomass.
2 Assuming 5 kcal/g dry weight.
3 All U.S. energy statistics are from this source.


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  • EIA (Energy Information Administration). 2001. Annual Energy Review 2001. Washington, D.C.: U.S. Department of Energy. Available online at:
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  • IPCC (Intergovernmental Panel on Climate Change). 2001. Climate Change 2001: The Scientific Basis. Contribution of Working Group I to the Third Assessment Report of the Intergovernmental Panel on Climate Change. New York: Cambridge University Press.
  • Kataoka, N., A. Miya, and K. Kiriyama. 1997. Studies on hydrogen production by continuous culture system of hydrogen-producing anaerobic bacteria. Water Science and Technology 36(6-7): 41-47.
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TABLE 1 Biological Reactions That Yield Potential Fuels
Net ReactionRepresentative Organism
sugar --> ethanol + carbon dioxide

hydrogen + carbon dioxide --> methane + water

sugar + water --> hydrogen + acetic acid + carbon dioxide

acetic acid --> methane + carbon dioxide

carbon monoxide + water --> hydrogen + carbon dioxide

lactic acid + water --> hydrogen + carbon dioxide

H+ + ferredoxin-1 --> hydrogen + ferredoxin0

Methanococcus jannaschii

Clostridium burtyricum


Carboxydothermus hydrogenoforma

Purple bacteria

Cyanobacteria, green algae
About the Author:Hamilton O. Smith is science director, Robert Friedman is VP, environmental and energy policy, and J. Craig Venter is president at the Institute for Biological Energy Alternatives in Rockville, Maryland.