Chapter 6
The Future Under a Microscope

A bacterium was the birthplace of genetic engineering, one of the most revolutionary technologies in science. And since those first experiments with bacteria back in the 1960s, hundreds of new medicines and products have become commonplace. But genetic engineering is only the tip of the microbial iceberg. To understand how microbes work in the world around us and how they affect our lives, scientists are recording their entire genetic code.

Writing the Book of Bacteria

In 1994 the U.S. Department of Energy (DOE) announced the beginning of the Microbial Genome Project. A genome is the complete set of instructions for making any organism. It is the "parts list" of the organism's DNA—the list of letters that represent the base pairs that make up the DNA strand. A single microbial genome may contain between 500,000 to 8 million DNA base pairs; the human genome contains 3 billion. Whereas the Human Genome Project took years to write the "first draft" of the entire genetic material inside a person's cells, most microbes can be sequenced in a matter of weeks or even days. By the end of 2003, more than one hundred bacteria and viruses had been sequenced.

But why would the DOE want to know every letter in the long DNA sequence of a microbe? Scientists want to know because these letters hold the code for the creation of certain proteins that carry out various functions within the cell. Some genes instruct the production of certain proteins to make the cell wall, while others instruct the cell to manufacture hydrogen or to infect liver tissue. But just as a parts list of a car's engine does not explain the assembly and function of the car, the genome does not provide information about what the parts do. Another project called Genome for Life, an extension of the Microbial Genome Project, is seeking to understand the function of the genes that have been written down.

According to Daniel W. Drell of the DOE and his colleagues, "We can now look at how the 'parts' come together in ways that challenge basic science and offer concrete applications in a range of issues affecting, for example, water quality, environmental remediation, and medicine."²⁶ The hope is that microbes will prove to be a source of new genes that can be used to solve problems that confront society today. The DOE is most interested in microbes that can address environmental problems, such as global warming and toxic waste cleanup, or lead to new sources of clean, environmentally friendly energy.

Global Warming

Over the past decades scientists have found that Earth's temperature is rising more rapidly than expected, and they predict another rise of 1.5 to 4.5 degrees centigrade over the next one hundred years. This rise in temperature is due to the increased amount of carbon dioxide (CO₂) and other greenhouse gases that are released into the atmosphere from industrial processes. They eat away at the ozone layer, which protects the earth from the sun's harmful rays. Coupled with changing land use and deforestation, these gases have long-term effects on the planet. Increased temperatures can lead to a rise in the ocean's water levels, which erodes coastlines. It could trigger floods and drastically change ecosystems.

But what if there were microbes that ate excess CO₂? In 1991 two Japanese microbiologists who were exploring ways to maintain the atmosphere discovered a bacterium called Synechococcus, which thrives on CO₂. The scientists believe that knowing the genome of CO₂-consuming bacteria could lead to the future development of huge bioreactors filled with bacteria feeding off of unwanted CO₂ in the atmosphere.

Extreme Genes

Many of the microbes that the DOE researchers have selected for the genome project live in extreme places. "The diversity and range of their environmental adaptations indicate that microbes long ago 'solved' many problems for which scientists are still actively seeking solutions."²⁷

For example, the bacterium Methanococcus jannaschii grows in thermal vents eight thousand feet below the ocean off the coast of Baja California. It thrives under high pressure and temperatures as hot as 190 degrees Fahrenheit. It exists in anaerobic conditions and produces methane gas. M. jannaschii is being studied as a working model for the production of methane as a useful, renewable energy source.

When scientists know the code for what makes a bacterium operate, they will also know how to control it. And comparing the genomes of one bacterium to another will allow scientists to see patterns of function and predict what other microbes are capable of doing.

So far the genome researchers have been awed by the amount of previously unidentified genes they have uncovered from some of these extreme microbes. More than half of the genes sequenced in M. jannaschii, for example, were completely unknown to science. This means that the proteins that the genes instruct the cell to create are also unknown. They offer an amazing new resource to explore. The genome project is bringing to light a vast menu of genetic ingredients of genes and proteins that can be used to genetically engineer new microbes and new products.

The DOE is not the only place that is sequencing the genes of microbes. Medical institutions focus on the bacteria and viruses that cause disease. If scientists can figure out which genes are responsible for the cause and means of infection, then they can target those genes with drug therapy.

A Vaccine for Cancer

Most people think of a virus as something that should be avoided, but for years we have used weakened forms of viruses to combat smallpox, polio, chicken pox, measles, and mumps. Now researchers are hoping to add cancer to that list.

Emptied of its contents, a virus's capsid becomes a durable container capable of withstanding all sorts of toxic environments and able to transport many different chemicals and drugs to a specific location. Viral containers are already being used to deliver magnetic material to tumor cells so that they can be seen in magnetic resonance imaging (MRI) tests, and they are now being tested for use in delivering cancer cures.

The part of a virus that makes it a perfect medical tool is its ability to target a specific type of cell. The drugs currently used to treat cancer circulate throughout the entire body. They act on healthy cells as well as cancerous cells, causing many side effects that can be quite severe. But viruses are very specific. They target only the cells they are programmed to infect and leave other cells alone. Scientists around the world are looking at ways to use the virus's natural targeting characteristic to zero in on specific cancerous tumor cells.

At the Institute for Cancer Studies at Birmingham University in England, researchers are working on an experimental therapy using a genetically modified virus as a homing device for cancer-killing drugs. It is called VDEPT, short for virus-directed enzyme prodrug therapy.

A patient would first be injected with the specially designed virus that infects only cancer cells. Then an injection of the prodrug is given. The prodrug is a chemical that is harmless to healthy cells, but when it comes in contact with the virus-infected cancer cell, it becomes deadly. The cancer cells take it in, and the drug is transformed into a toxic substance that kills the tumor cell instantly. Healthy cells remain unaffected.

Virus Vectors

Scientists are experimenting with viruses not only to distribute a needed vaccine but also to deliver healthy

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genes to cells with a genetic disorder, a procedure called gene therapy. Gene therapy could help patients who have a genetic disorder like cystic fibrosis or sickle-cell anemia, where only one or two missing or defective genes are involved.

In gene therapy RNA retroviruses are first rendered harmless. Then the healthy genes are inserted into the virus's genome. The altered virus is then injected into the tissue where it actively seeks out the appropriate cells to infect. As the RNA is copied by the cell's reproductive machinery, it is also incorporated into the cell's DNA.

This procedure is still in an experimental stage, but one of the first patients to benefit was an eighteen-month-old boy in England. He had a rare genetic disorder called severe combined immunodeficiency that prevented him from developing an immune system. He lived his first eighteen months in a plastic, sterile bubble room. Doctors removed bone marrow from the boy and used a virus to carry a new working version of the missing gene into immune cells in the marrow. The marrow was put back into the boy's leg, where it gradually started to produce healthy white cells that now protect the boy from infection.

One problem doctors must overcome is the unpredictability of where the new gene is inserted in the patient's DNA strand. If the placement is not exact, then the gene will not express itself. Scientists also have to battle with the patient's immune system, which seeks out and destroys these virus vectors before they get a chance to deliver their genetic package.

Even though gene therapy is still in the experimental stage, it has caused much controversy. Many people are concerned about the safety of the procedure as well as the long-term effects of inserting a virus, even a disabled one, into a person's body.

Nanotechnology

Viruses are making their mark in industry too, where they are being used as spare parts and miniature tools

in the growing field of nanotechnology. Nanotechnology is the term given to research and engineering done at an atomic or molecular level. Nano means one-billionth, and a nanometer is one-billionth of a meter.

Small is big in science. When Nobel Prize–winning physicist Richard Feynman declared in 1960, "There's plenty of room at the bottom,"²⁸ he meant that technology can always get smaller. In 1946, when the first computer was constructed, it filled two thousand square feet of space and weighed fifty tons. Today the smallest microcomputer would fit on the head of a matchstick, and the smallest microchip, unveiled in 2003 by a Malaysian company, is no bigger than the period at the end of this sentence. But the smaller technology gets, the more necessary it becomes to study those organisms that perform complex tasks on that level every day—microbes.

"Scientists didn't invent nanoscience," says Angela Belcher, a pioneering materials chemist at Massachusetts Institute of Technology. "Organisms have been doing if for a long time."²⁹

Belcher started out studying how sea snails made their beautiful mother-of-pearl shells. The snail stacks individual molecules of calcium carbonate into layers to form a beautifully luminescent and very strong shell. Belcher uses the same technique of building a new material molecule by molecule, but she gets viruses to do the hard work for her.

Viruses make a good workforce because they have evolved over millions of years to work perfectly at the nanoscale level. It is also easy to alter a virus's genetic material and instruct it to perform a specific task. The viruses that Belcher and most nanoscientists use are bacteriophages because they infect only bacteria. These viruses are genetically modified to grow certain protein receptors on their surface so that they are able to bind like a magnet to specific particles. This process takes about three weeks.

One such virus strain is able to bind to zinc sulphide, a semiconductor, which means it can transmit an electrical current. Billions of these specially made viruses bind to billions of zinc particles. In a solution, viruses normally organize themselves in almost military precision so that they move freely without bumping into one another or creating a logjam. As these viruses with their zinc particles self-organize, they form an extremely thin film that can be picked up out of the solution with a pair of tweezers. This thin film acts like the liquid crystal display on computer monitors. Belcher believes that her viruses can create stronger, smaller, and potentially more complex materials than those produced by man-made machines. The process is also clean; it does not pollute the environment.

In another lab researchers are working to perfect viral wire. The bacteriophage viruses are altered to bind to other particles, but only at the ends of their long, skinny bodies. They latch on to each other, end to end, like children's snap-together beads, forming long chains of microscopic semiconducting wire.

Silver-Making Bacteria

Creating any kind of material on a nanoscale is costly and complex, but if bacteria can collect particles of a precious metal like silver, it could be invaluable. In a Swedish laboratory, scientists are working with an unusual strain of bacteria that does just that. They crank out tiny crystals of silver.

Silver is usually toxic to most microbes and is used in several bacteria-killing substances, but Pseudomonas stutzeri seems to thrive on it. This bacterium, which is the same microbe that is used to clean paintings, was found growing on rocks in a silver mine. The bacterium gathers up the metal and bundles it in distinct crystal shapes at the edge of its cell. These microscopic silver particles can then be harvested to construct extremely thin, light-sensitive metal film or coatings for solar collectors, or tiny optical and electronic devices.

Bacterial Batteries

How could a tiny electronic device made out of microscopic particles of silver be powered? Some researchers are taking their cue from the science fiction Matrix movies, in which humans are used as living batteries, and learning how to harness a living electrical source. Fortunately they are not using humans, as the movies portray; instead, they are creating microbial fuel cells and bacterial batteries.

Like any living organism, bacteria take in and expel energy. A colony of E. coli bacteria takes in carbohydrates, such as sugar, and breaks them down with enzymes. The bacteria release energy in the form of hydrogen, the same substance that fuels "green" cars. The electrical current comes in the form of a steady flow of electrons released as the microbe eats.

One company in England has made a fuel cell that is the size of a personal CD player. The bacteria inside feed on sugar cubes. Chemical reactions strip electrons from the hydrogen atoms to produce a voltage that can power an electrical circuit. To make it more cost-effective, researchers are developing a second model that would be fueled by organic waste material, such as the leftovers from lunch. Currently, the microbial fuel cell is being used to power a small robot around the lab.

The U.S. Department of Defense is interested in another microbial fuel cell that uses a bacteria found on the bottom of the sea floor. Rhodoferax ferrireducens can convert more than 80 percent of the sugar it eats to electricity. The process is slow. One cup of sugar can light up a 60-watt bulb for seventeen hours, but the process to do so takes a week to charge up. The advantage to this slow process is that once it gets going, the battery continues to work without interruption—a good quality to have in a battery that is difficult to access. The Department of Defense is eyeballing microbial fuel cells to power electronic monitoring devices located at the

bottom of the ocean. These fuel cells would run off of the organic sediment found on the sea floor.

Other fuel cells are being adapted to power medical ventilators and generate electricity for pacemakers. The pacemaker battery would run off of glucose, the sugar found in the pacemaker-wearer's blood.

Microbial Motors

Imagine a microscopic device propelled by a nanoscale motor that could buzz through the body in search of specific cells. That is the target goal for engineers at Cornell University. Researchers combined a molecule made by a bacterium with one made by a scientist in the lab. The result was a motor that operates similarly to an E. coli bacterium turning its flagella on and off.

The E. coli uses the enzyme ATP to send signals to its flagella so that it can move around. Instead of flagella, researchers attached an engineered nanoscale rotor to act as the motor's moving part. The rotor rotates in response to electrochemical reactions with charged parts of the ATP molecule. This specially designed E. coli bacterium could be tethered to a fixed spot and used as a tiny pump in industrial and medical devices.

The Future

Powering pacemakers with a bacterial battery, curing cancer with a virus, or cooking over a gas stove fueled by methane-producing microbes from the backyard septic tank may seem far-fetched, but they could become common events in the future.

Each year we become more aware of the influence of the mighty microbe. Looking into the past, we see that microbes have had the power to change human history. Experiencing the infectious diseases of today, we know that microbes can end a person's life, diminish a village's population, and devastate a country's economy. But they can also be the solution to many of our problems in the future.

Whatever our technology needs may be or whatever problems confront us—from emerging disease to environmental

damage—there will be a microbe somewhere that is able to help, but only if people are wise enough to discover it. Such discoveries will take time. Scientists have only been aware of bacteria and their effect on humans for less than three hundred years. And they have only scratched the surface of the world of viruses. Their understanding of these microorganisms and their power continues to grow, along with an appreciation of what man and microbe can do together. Researchers can learn how to maintain the atmosphere from studying bacteria that have been doing just that for millions of years, and medical doctors can discover how to keep people healthy by examining the viruses that infect them.

The key to harnessing bacteria and viruses for good is to appreciate the possible consequences of the bad, because our relationship with the microbial world is a two-way street. Humans' behavior affects microbial behavior, and vice versa. We might not see the next devastating infectious bacteria or virus barreling down on us, but with the use of other microbes, we will have the tools and knowledge to combat it. It is simple. Bacteria and viruses are our worst enemies, yet they are also vital for our survival. We live in a sea of invisible microbes, and we can either sink or swim.