Allies and Enemies: How the World Depends on Bacteria (26 page)

the Earth’s oil and subsurface bacteria. Some bacteria live in a world

flooded with hydrocarbons, intense pressure at two and a half miles

deep, and temperatures of 185°F: the world’s oil reserves. The earliest studies on species recovered from the reserves revealed that many were related to surface species, surprising since the oil bacteria have been sealed off from other life for 200 to 500 million years. To defuse the inevitable charges of contamination that skeptics made toward this discovery, scientists have constructed small sampling capsules that open only when they reach oil and enclose their sample before returning to the surface.

A new science in oil microbiology has begun. Bacteria will play a

pivotal role in oil refining, invention of fossil fuel alternatives, and oil spill cleanup. Microbiology has plans for the bacteria that live on oil.

By analyzing the genes of bacteria recovered from oil and comparing

them to genes in soil species at the surface, biologists may be able to locate new oil reserves. A similar array of genes between both groups could indicate that the surface microbes are living on oil seepage from oil reserves below them.

The relationship between oil and global ecology, or macrobiology,

is complex. But at the core of oil’s origin and its future sit the bacteria.

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Climate, bacteria, and a barrel of oil

A band of rock called the Isua formation runs along the edge of an

inland ice cap from western Labrador to southwestern Greenland.

The formation holds the oldest known rock found so far on Earth, dated at 3.8 billion years. Traces of fossilized life lace the Isua formation and analyses of its carbon content point to photosynthetic ancestors of cyanobacteria.

During the period in which the Isua formation developed, the

Earth’s atmosphere held no oxygen. Primitive photosynthetic

microbes used the sun, carbon dioxide, and the Earth’s elements (nitrogen, sulfur, phosphorus, salts, and metals) to sustain life. Their rudimentary photosynthetic reactions released little oxygen. Chemically unstable compounds in the atmosphere quickly captured what

little oxygen the microbes liberated, and the oceans absorbed the rest. By 2.2 billion years ago, however, the oceans had accumulated enough dissolved oxygen to allow the gas to begin building up in the

atmosphere. The oxygen levels in the atmosphere began to stabilize

about 2 billion years ago.

Evolution is a change in an entire population due to small and discrete adaptations that favor species survival. The accumulation of oxygen on Earth signaled the development of a stable population of

photosynthetic microbes that we now identify as primitive cyanobacteria. The cyanobacteria split into two evolutionary paths at least two billion years ago. One branch gave rise to plants. (Gene analysis suggests that the archaea branched off this path.) The second branch led to modern cyanobacteria and other bacteria.

By analyzing bacterial DNA, scientists have found that almost all

bacteria contain DNA base sequences that are remnants of earlier 145

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evolutionary paths. In other words, bacteria have exchanged genes for so long that their evolution may resemble more of a network than a straight path. A few microbiologists have half-jokingly proposed that instead of estimating the thousands of bacterial species in the world, we should think of all bacteria as belonging to one giant species with a huge family tree of relatives.

The evolution of photosynthesis by whichever multiple paths it

used accelerated the development of other biota. Microbial ecologist

Patrick Jjemba has justifiably concluded, “The evolution of photosynthesis is the most important metabolic invention in the history of life on Earth.” Bacterial diversity increased as oxygen levels rose from 0.1

percent (about 2.8 billion years ago) to 1 percent (2 billion years) to 10 percent (1.75 billion years). Not until the Cambrian Period, 543 to 490 million years ago, did oxygen reach its present concentration.

The sudden increase in the diversity of life has prompted scientists to call it the Cambrian Explosion. The evolution of today’s higher plants and animals took less time than the evolution of the Earth’s first bacterial cell.

Although life developed into hundreds of millions of different

forms, the variety of aerobic or anaerobic energy-production schemes

inside cells remained disproportionately small. The pathway called glycolysis is life’s universal pathway because it exists in every living thing. Bacteria use glycolysis as humans and other animals do by getting a small amount of energy from the breakdown of glucose to pyru—vate. After glycolysis, various bacteria use a varied but limited choice of metabolisms. In addition to photosynthesis and glycolysis, bacteria use anaerobic fermentations, anaerobic or aerobic respiration, plus a

small number of specialized metabolisms that branch off from these

main metabolic pathways.

The story of oil began when oxygen accumulated in the atmosphere and fed the respiration of aerobic organisms. Food chains made

of a widening diversity of life developed on continents and in the oceans. Bacteria, protozoa, algae, worms, and crustaceans built a hierarchy of prey and predators. The oceans took in dead bacteria, invertebrates, plankton, and the remains of prehistoric multicellular creatures. The majority of expired macro-and microscopic life never

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reached the ocean floor; other animals ate the organic matter as it sunk. But over millennia the populations of marine organisms

increased, and more organic matter drifted down and built up in the

sediments under the ocean.

The diversity of species that ended up in the organic sediments

contributed to sediments’ various forms of carbon. The Earth has been estimated to hold at present about 1.4 million known species and at least 10 times that number of undiscovered, uncharacterized species. Many times more species have already gone extinct than the

number that survive today, yet today’s biodiversity resulted directly from the Cambrian Explosion, the period in Earth’s history when oxygen systems expanded faster than anaerobic systems.

The story of oil

Plant and animal matter decomposed due to the action of bacteria millions of years ago as it does today. As each layer of organic matter under the ocean crushed the layers below, the pressure expelled water molecules. The sediments accumulated a dense mixture of carbon compounds, the majority of which were hydrocarbons, long carbon chains in which each carbon is saturated with hydrogen. Over millions of years, the pressure pushed the hydrocarbons deeper into the Earth and caused them to harden into a brownish-black solid. A

chunk of this material viewed through a microscope would reveal fossilized bacteria—hence the name fossil fuel—with other bits of plant life, marine invertebrates, and shells.

Oil formation from the hard, black material required a precise combination of organic substances, pressure, time, and characteristics of the surrounding rock. Pressure from above pushed clumps of organic matter toward the Earth’s center where it rose to about 180°F. Given enough time, the heating and the pressure turned the black rock into a liquid in which the hydrocarbon chains broke into a

heterogeneous mixture of smaller chains. The pressure then pushed

the liquid into pores in the surrounding rock. As the liquid squeezed

through the network of pores, membrane constituents from bacteria

mixed with it and increased its water-repelling property. The entire

process produced crude oil.

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At about 18,000 feet deep, oil remains in liquid form. Deeper, the

intense pressure and heat further decompose the hydrocarbons into

methane or natural gas. At shallower depths, the hydrocarbons

remain solid and make up coal.

Microbiologists know that bacteria have played an integral part in

formation of fossil fuels, but they still do not know all the ways in which bacterial metabolism altered oil’s hydrocarbon composition from site to site. Oil shale, the rock that contains crude oil in a network of pores, contains chlorophyll pigments resembling those of modern photosynthetic bacteria. The late microbial ecologist Claude ZoBell has added that without bacteria oil would never have been formed. ZoBell theorized that subterranean bacteria acted on the longest hydrocarbons to make shorter (but still long) hydrocarbons.

Crude oil contains hydrocarbon lengths from 8 to 80 carbons, and the

relative composition varies between reserves and within the same reserve. For centuries, hydrocarbon-digesting anaerobic bacteria saturated the carbon atoms with hydrogen. These anaerobes also helped form natural gas, the very same methane produced inside ruminants

and termites.

Fossil fuels can be viewed as renewable resources because the

sedimentation process is continual. Organic matter continues to sink

underfoot, and bacteria will eventually make more oil. But the process unfolds on a timescale that humanity does not comprehend.

Most people should by now understand that the rate of oil consumption outpaces the Earth’s available oil. Saudi Arabian oil expert

Sadad I. Al Husseini calculated in 2000 that the world’s oil reserves

would level off about the year 2004, and the plateau might last for no

more than 15 years. After this plateau, the remaining oil becomes too

difficult and/or too expensive to extract. The United States already passed this Rubicon in the early 1970s. A clue that signaled an oil deficit arose during that decade: increasing numbers of oil tankers bringing crude to the United States from halfway around the globe, often accompanied by spills.

Bacteria can help build second and third generations of alternative energies. Could bacteria be engineered to manufacture hydrocarbon fuels on a scale needed by the human population?

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Bacteria power

Unrefined crude oil poisons marine and terrestrial animals that ingest

it. Oil’s aromatic hydrocarbons, compounds with a carbon ring structure (benzene, toluene, xylene, and so on) damage tissue, enzymes, and nervous systems. Bacteria view crude oil as a carbon-rich and digestible food. Bioengineers have begun to turn to this process on its head.

Entrepreneurial companies such as LS9 in California have bioengineered E. coli and other bacteria to produce hydrocarbons that refineries can then turn into fuel without emitting sulfur gases made by conventional refineries. Microbiologists know how to make a minor

alteration to bacterial fatty acid synthesis so that the cells produce gasoline instead of fats. Bioengineered species might soon churn out hydrocarbons of specific chain lengths as a way to adjust octane level.

The proportion of heavy, hard-to-extract oil has risen in oil

reserves as Big Oil draws off the lighter, cleaner crude. Geomicrobiol—

ogists now search for bacteria that convert heavy oil to higher quality fuel for combustion engines. Increasing today’s oil recovery rate by as little as 5 percent would make a substantive impact on world oil supply.

The bacteria that fix nitrogen, that is, capture nitrogen gas

directly from the air, release hydrogen gas, which has been touted as

an alternative to fossil fuel. Heterotrophs, some photosynthetic bacteria, and anaerobes make hydrogen as part of their normal metabolism. Bacterial hydrogen production for future fuels would require large fermenters designed to allow in sunlight for photosynthesis and possibly more than one species working in concert. For example an

anaerobe that produces hydrogen might pair with anaerobic photo—

synthetizers that energize the system by absorbing sunlight.

Current chemical methods for making hydrogen involve breaking

apart water molecules in a costly and technologically challenging process. Bacteria use the enzyme hydrogenase to split water into hydrogen and oxygen with less energy demand than the same reaction in a manufacturing plant. Some bacterial hydrogenases need only a small supply of selenium, iron, and nickel to stabilize the reaction.

Biochemists are already working on a thermophile Clostridium that performs the reaction at about 140°F and dispenses with the need for added metals.

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Oxford University chemists have also attached hydrogenase and a

light-sensitive dye to microscopic titanium dioxide beads. In this system, photosynthetic microbes supply their own energy by capturing solar energy. No conventional chemical companies can make the