Allies and Enemies: How the World Depends on Bacteria (21 page)

GMOs fitted with the genes from native bacteria that degrade

fuels, pesticides, industrial solvents, and toxic metal compounds have

been developed in microbiology laboratories all over the world. Government agencies have slowed this progress by limiting GMOs to experimental study rather than real-life environmental disasters. The U.S. Environmental Protection Agency reserves the term “bioremediation” for pollution cleanup by unaltered native bacteria and not

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bioengineered strains. Communities may be nearing a point at which

they must choose between hazardous substances in their environment and GMOs released to clean up those substances.

Biotechnology critics have warned of a future in which foods

come from 3,000-gallon vats of bacteria. Economic and technology consultant Jeremy Rifkin has cautioned that bacteria will make soil and farms obsolete. I am not sure how this could ever happen. I suspect Rifkin is speaking in metaphor to warn us of GMO-produced foods that could supplant traditional agriculture. Rifkin’s Web site warns also that “the mass release of thousands of genetically engineered life forms into the environment [will] cause catastrophic genetic pollution and irreversible damage to the biosphere.” Biotechnology today must stand up to strong criticism even as it develops new life-saving drugs and invents processes that clean the environment.

The concept of developing microbial food for humans relates

mainly to single-cell protein, or the use of microbial cells as a dietary protein supplement. This idea is at least 20 years old and had been proposed as a way of alleviating global hunger and protein deficiency.

Single-cell protein from bacteria never reached practical levels for two reasons. First, bacteria grown in large quantities as a food must be cleared of any toxin or antibiotic they might make, which complicates the production process and raises costs. Second, microbial products packaged as a protein-dense food would likely induce serious allergic reactions in many consumers. Bacteria cannot replace traditional agriculture even if a future generation of scientists found a way to do it. The Earth needs green plants as much as it needs bacteria.

Warnings by biotech’s critics about GMOs invading natural

ecosystems continue. Bacteria are survivors because of supreme

adaptability. Could the adaptability needed by a GMO to carry out its

job in nature also allow the microbe to take over ecosystems? Natural

ecosystems possess exquisite mechanisms to ensure balance between

competitive species from bacteria to higher organisms. Motility, quorum sensing, spore formation, and antibiotic production are examples of the many devices bacteria use to ensure they receive adequate habitat, nutrients, and water. A GMO must overcome all competitors to take over an ecosystem, but nature long ago developed mechanisms to protect the balance of species and resist drastic change. It is chapter 5 · an entire industry from a single cell

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wise to remember also that bacteria have been exchanging genes that

help them survive since the beginning of their existence. Most new

genes that become part of a cell’s DNA by either gene transfer or mutation give no benefits to the cell. Because the genes of GMOs are designed to accomplish very specific tasks, the chances of a GMO ruling over natural communities seem remote.

The National Institutes of Health (NIH) have published hundreds

of pages of regulations on GMOs with the intent of reducing the chances of a GMO accidentally escaping into the environment. These

rules cover methods for containing recombinant microbes by physical,

chemical, and biological tactics. Current physical containment

involves the safe handling and disposal of GMOs so that live cells do

not accidentally escape a laboratory and enter an ecosystem. Microbiologists use special safety cabinets based on the principles of BSL-4

cabinets. They also sterilize all wastes before discarding them. Chemical methods include disinfectants and radiation to kill bacteria in places they might have contaminated. But the dexterity with which bacteria evade chemicals—imagine the consequences of a GMO

lodged inside a biofilm—highlights the weaknesses of chemical containment. To date, biological methods for making GMOs safe in the

environment offer the greatest promise.

Microbiologists can engineer bacteria to self-destruct by adding

suicide genes to recombinant DNA. Suicide genes control GMOs

after the microbe has completed its task. The safety mechanism works by either positive or negative control. In both cases, a second compound, or activator, keeps the suicide gene from working until conditions change in the environment. In positive control, a chemical or other stimulus such as a certain temperature, affects the activator, which then releases its control over the suicide gene. The now active suicide gene initiates a progression of events in the cell that lead to its death, a process called apoptosis. In the hypothetical example already mentioned, a 3,000-gallon batch of bioengineered E. coli making growth hormone, ruptures and spills in a 7.0 Richter earthquake—a

believable event in California where hundreds of biotech companies

exist. The E. coli might rush into nearby soils and streams, producing hormone that traumatizes ecosystems. But a suicide gene designed to turn on when cells are exposed to a temperature of 72°F or lower—fermenters usually run at about 100°F—ensures that the E. coli

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destroys itself as soon as it escapes into the environment. Negative control turns on when a stimulus in the environment disappears.

Bioremediation bacteria designed to degrade a pollutant, for example, undergo apoptosis when the pollutant disappears.

E. coli is the world’s most bioengineered microbe and also provides suicide genes for other GMOs. The gef gene in E. coli encodes for a 50-amino acid protein, small by protein standards, that turns on apoptosis in several different bacterial species. The gef gene has already been investigated as a treatment against melanoma cells and breast cancer, and for controlling engineered Pseudomonas. Bioengineered P. putida degrades alkyl benzoates, which are thickeners used in cosmetic products and drugs. As long as this pollutant remains in the environment, P. putida equipped with E. coli’s gef gene continues breaking it down. When the pollutant level has been reduced, the gef protein interferes with the normal flow of energy-producing electrons in P. putida’s membrane. The bioengineered Pseudomonas commits suicide.

Biological containment systems control GMO cells from within

the cell and thus promise the best method of preventing GMO accidents. But one P. putida cell per every 100,000 to 1,000,000 per generation is a mutant that resists the gef gene’s action. Will the clones win or will the mutants win? Biotechnologists have helped push the odds in favor of “good” clones over “bad” mutants by inserting two gef genes into P. putida, which lengthens the odds of resistance to one cell in every 100,000,000.

Anthrax

If E. coli is the world’s most bioengineered bacterium, Bacillus anthracis is the most feared because it causes the disease anthrax. B.

anthracis joins various viruses, parasites, other bacteria, and toxins (made by bacteria or fungi) on a list of potential bioterrorism threats.

Not only does the B. anthracis toxin cause lethal effects in humans, but the bacterium’s ability to form endospores helps it out-survive other pathogens. Endospore-formation keeps the cells alive and yet resistant to chemicals, irradiation, and antibiotics.

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B. anthracis begins as a laboratory culture like other bacteria. To make endospores, a microbiologist stresses the cells by heating the culture broth. The cells begin forming endospores within minutes of this stress. The microbiologist can freeze-dry the spores to make a brown to off-white powder; the color depends on the type of medium that had been used for growing the cells.

The dry, odorless, and lethal powder has caused significant concern

in the United States, especially since anthrax was used as a presumed

weapon distributed in mail in 2001. Security teams at airports and public buildings now search for unidentified powders as possible anthrax.

As a bioweapon, other pathogens work better than anthrax. The

pathogen causes illness if it enters the body through a wound in the

skin, by ingestion, or inhalation, with inhalation being the likely route of infection for a bioweapon. The skin route would be impractical for a terrorist and putting anthrax into food or water becomes ineffective

because of a phenomenon called the dilution effect. Community

water supplies and food products contain such large volumes that a

terrorist would find it impossible to contaminate either with a dose

big enough to kill. The endospores require a large dose to cause infection in people, so food and especially water would dilute them to harmless levels. A terrorist would furthermore be hard-pressed to

perform the laborious culturing and freeze-drying steps needed to make a significant amount of endospores.

Disease by inhalation has caused greater concern because it has

already been shown to cause most anthrax cases, the contamination of

postal letters in 2001, for instance. But not everyone who gets infected develops disease. People who do get sick cannot transmit it to others because anthrax is noncontagious. Even though B. anthracis grows easily in a laboratory, all other characteristics of this microbe make it a poor bioweapon. Therefore, the most feared bacterium is not as big a threat to a large population of people as many believe.

Why we will always need bacteria

White biotechnology offers the greatest hope of integrating bacteria into industry in a way to positively affect the environment. The use of bacteria to perform activities now carried out by strong acids and 118

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organic solvents will drastically cut down on the chemical wastes flowing into rivers, soils, and groundwaters. Many industrial steps must take place at several hundred degrees, which consumes large amounts of energy. Bacteria substitute biodegradable enzymes for caustic chemicals and work at mild temperatures, and they do it quietly. Microbial fermentations also produce heat that can be rerouted into the manufacturing facility to reduce overall energy use.

Bacteria are white biotech’s raw material. Rather than watch truck

or trainloads of chemicals roll toward manufacturing plants, neighbors of a white biotech company might spot a person carrying a single vial of freeze-dried bacteria. From that point, the bacteria regenerate themselves. In fact, ancient societies might wonder why present-day industry bothers with their noxious mix of materials and wastes. Bacteria already make almost every compound humans find important, even plastic. Pseudomonas species make polyesters called polyhydroxyalkanoates (PHAs) from sugars or lipids found in nature. The bacteria use the large compounds as a storage form of carbon and energy and as the sticky binder in biofilm.

Industrial interest in PHAs increases or decreases with oil prices

because oil serves as a cheap precursor for making most plastics. As

oil prices rise, PHAs become more attractive for making soft containers such as shampoo bottles. But PHA production is not inexpensive due to the costs of nutrients for growing the bacteria and methods for

harvesting the polymer.

Bacillus megaterium and Alcaligenes eutrophus lead a group of diverse species that produce nature’s most abundant PHA, polyhydroxybutyrate (PHB). Bacteria excrete higher amounts of PHB under stress, probably as a protective coating around the cells. The narrow environmental conditions that induce the bacteria to turn on their PHB genes make this a very expensive natural product compared

with plastics derived from fossil fuels. PHBs are compatible with human tissue because they do not cause allergic reactions, and they are pliable. These attributes make PHBs good choices for medical equipment such as flexible tubing and intravenous bags. To reach this promising future for biodegradable plastics, white biotechnology will

be called upon to find the secrets of bacterial metabolism that lead to the cost-effective production of PHAs.

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Some manufacturing processes have changed little since the

dawn of the Industrial Revolution. Of all aspects of society, manufacturing lags the furthest behind in converting traditional processes into more sustainable methods. For this important change to take place the most self-sufficient organisms on Earth might well lead the way.

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The invisible universe

The field of microbial ecology focuses on the role microorganisms play in all of nature. Microbial ecologists study bacteria in small habitats of a few dozen species as well as global systems that circulate elements through continents and oceans. These systems called biogeochemical or nutrient cycles make carbon, nitrogen, sulfur, phosphorus, and metals available for humans and all other life. Microbial ecology now includes technologies aimed at reversing global warming, pollution, and biodiversity loss.