Selasa, 02 September 2008



Archaea or Archaebacteria, common name for a group of one-celled organisms, many of which do not require oxygen or sunlight to live. Before the discovery of archaebacteria, scientists divided all living organisms into prokaryotes (organisms without a cellular nucleus), which consisted primarily of bacteria, and eukaryotes (organisms with a cellular nucleus), which consisted of fungi, plants, and animals. Archaebacteria were initially grouped with bacteria because like bacteria, they lack a well-defined nucleus. Recent evidence, however, has demonstrated that archaebacteria have a genetic makeup that more closely resembles the eukaryotes, organisms that have a well-defined nucleus. This unique structure means that archaebacteria cannot be accurately grouped with either the prokaryotes or the eukaryotes. Instead, scientists have proposed that these microorganisms be classified in a new branch of life, or domain, called archaea.
Archaebacteria often live in extreme conditions that were once considered inhospitable to life. Some archaebacteria live in deep-sea hydrothermal vents in the Pacific Ocean. Located at depths of 3 km (2 mi), the hot vents provide a dark environment with extremely high temperature and pressure where few creatures can survive. Instead of deriving energy from the sun, these microorganisms obtain energy by oxidizing inorganic chemicals that spew from the hot vents. In a process known as chemosynthesis, archaebacteria harvest energy from chemical reactions involving hydrogen sulfide and other inorganic compounds. These deep-sea archaebacteria make up the bottom of the food chain for clams, tube worms, mussels, and other animals that live near the vents (see Marine Life).
Scientists initially found archaebacteria only in harsh environments, but recently these microorganisms have been found in the guts of animals, compost piles, saturated marshes, and other common places. Knowledge gleaned from studying a third branch of life could provide insight on the common ancestry of all living organisms.
Scientific classification: Archaebacteria are members of the domain archaea. The archaebacterium found near deep-sea hydrothermal vents is classified as Methanococcus jannaschii.

Bacteria, one-celled organisms visible only through a microscope. Bacteria live all around us and within us. The air is filled with bacteria, and they have even entered outer space in spacecraft. Bacteria live in the deepest parts of the ocean and deep within Earth. They are in the soil, in our food, and on plants and animals. Even our bodies are home to many different kinds of bacteria. Our lives are closely intertwined with theirs, and the health of our planet depends very much on their activities.
Bacterial cells are so small that scientists measure them in units called micrometers (µm). One micrometer equals a millionth of a meter (0.0000001 m or about 0.000039 in), and an average bacterium is about one micrometer long. Hundreds of thousands of bacteria would fit on a rounded dot made by a pencil.
Bacteria lack a true nucleus, a feature that distinguishes them from plant and animal cells. In plants and animals the saclike nucleus carries genetic material in the form of deoxyribonucleic acid (DNA). Bacteria also have DNA but it floats within the cell, usually in a loop or coil. A tough but resilient protective shell surrounds the bacterial cell.
Biologists classify all life forms as either prokaryotes or eukaryotes. Prokaryotes are simple, single-celled organisms like bacteria. They lack a defined nucleus of the sort found in plant and animal cells. More complex organisms, including all plants and animals, whose cells have a nucleus, belong to the group called eukaryotes. The word prokaryote comes from Greek words meaning “before nucleus”; eukaryote comes from Greek words for “true nucleus.”
Bacteria inhabited Earth long before human beings or other living things appeared. The earliest bacteria that scientists have discovered, in fossil remains in rocks, probably lived about 3.5 billion years ago. These early bacteria inhabited a harsh world: It was extremely hot, with high levels of ultraviolet radiation from the sun and with no oxygen to breathe.
Descendents of the bacteria that inhabited a primitive Earth are still with us today. Most have changed and would no longer be able to survive the harshness of Earth’s early environment. Yet others have not changed so much. Some bacteria today are able to grow at temperatures higher than the boiling point of water, 100oC (212oF). These bacteria live deep in the ocean or within Earth. Other bacteria cannot stand contact with oxygen gas and can live only in oxygen-free environments—in our intestines, for example, or in the ooze at the bottom of swamps, bogs, or other wetlands. Still others are resistant to radiation. Bacteria are truly remarkable in terms of their adaptations to extreme environments and their abilities to survive and thrive in parts of Earth that are inhospitable to other forms of life. Anywhere there is life, it includes bacterial life.


Much of our experience with bacteria involves disease. Although some bacteria do cause disease, many kinds of bacteria live on or in the human body and prevent disease. Bacteria associated with the human body outnumber body cells by ten to one. In addition, bacteria play important roles in the environment and in industry.

A. Bacteria and Human Health

We have all had bacterial diseases. Bacteria cause many cases of gastroenteritis, sometimes called stomach flu. Perhaps the most common bacterial disease is tooth decay. Dental plaque, the sticky film on our teeth, consists primarily of masses of bacteria. These bacteria ferment (break down) the sugar we eat to produce acids, which over time can dissolve the enamel of the teeth and create cavities (holes) in the teeth.

Tooth decay provides a good example of how multiple factors contribute to bacterial disease. The human body hosts the bacteria, the diet supplies the sugars, and the bacteria produce the acid that damages the teeth.

A1. Bacteria That Inhabit the Body

Communities of bacteria form what are called biofilms on many body surfaces. Dental plaque is a biofilm covering the teeth. Biofilms also cover the soft tissues of our mouths and the inner surfaces of our nose, sinuses, throat, stomach, and intestines. Even the skin has bacterial communities that extend into hair follicles. Bacterial communities differ in each region of the body, reflecting the environmental conditions in their specific region. Bacteria that inhabit the surface of the stomach, for example, must deal with extremely strong acid in the digestive juices.
Some regions in the interior of the body are sterile—that is, devoid of living organisms other than the cells of the body. Sterile regions include the muscles, the blood, and the nervous system. However, even these regions face constant invasion by bacteria. The body’s immune system is designed to rid the body of these invaders.
A healthy, balanced community of bacteria is extremely important for our health. Some of these organisms protect us from disease-causing organisms that would otherwise infect us. Animals raised in a completely germ-free environment, without any contact with bacteria, are highly susceptible to infectious diseases if they are exposed to the outside world. Bacteria in our bodies also provide us with needed nutrients, such as vitamin K, which the body itself cannot make. The communities of bacteria and other organisms that inhabit the body are sometimes called the normal microflora or microbiota.

A2. Disease-Causing Bacteria

In most cases the bacteria that cause disease are not part of the bacteria that normally inhabit the body. They are picked up instead from sick people, sick animals, contaminated food or water, or other external sources. Bacterial disease also can occur after surgery, an accident, or some other event that weakens the immune system.

A2a. Opportunistic Infections

When the immune system is not functioning properly, bacteria that usually are harmless can overwhelm the body and cause disease. These organisms are called opportunistic because they cause disease only when an opportunity is presented. For example, cuts or injuries to the skin and protective layers of the body enable normally friendly bacteria to enter the bloodstream or other sterile parts of the body and cause infection. Surgery may enable bacteria from one part of the body to reach another, where they cause infection. A weakened immune system may be unable to prevent the rapid multiplication of bacteria and other microorganisms.
Opportunistic infections became more important in the late 20th century because of diseases such as acquired immunodeficiency syndrome (AIDS), a viral disease that ravages the immune system. Also contributing to an increase in opportunistic infections is the wider use of cancer-fighting drugs and other drugs that damage the immune system.

A2b. Bacterial Killers

Some dramatic infectious diseases result from exposure to bacteria that are not part of our normal bacterial community. Cholera, one of the world’s deadliest diseases today, is caused by the bacterium Vibrio cholerae. Cholera is spread in water and food contaminated with the bacteria, and by people who have the disease. After entering the body, the cholera bacteria grow in the intestines, often along the surface of the intestinal wall, where they secrete a toxin (poison). This toxin causes massive loss of fluid from the gut, and an infected person can die of dehydration (fluid loss) unless the lost fluids, and the salts they contain, are replaced. Cholera is common in developing regions of the world that lack adequate medical care.
Another major bacterial killer is Mycobacterium tuberculosis, which causes tuberculosis (TB), a disease of the lungs. Tuberculosis is responsible for more than 2 million deaths per year worldwide. Although antibiotics such as penicillin fight many bacterial diseases, the TB bacterium is highly resistant to most antibiotics. In addition, the TB-causing bacteria readily spread from person to person.

A2c. New Bacterial Diseases

While tuberculosis and cholera have been with us for centuries, in recent decades new bacterial diseases have emerged. Legionnaires’ disease, a severe form of pneumonia, was first recognized at an American Legion convention in Philadelphia, Pennsylvania, in 1976. It is caused by a previously unknown bacterium, Legionella pneumophila, which is most often transmitted through infected water.
Lyme disease, a form of arthritis caused by the bacterium Borrelia burgdorferi, was first recognized in Lyme, Connecticut, in 1975. A bite from a deer tick that carries the bacteria transmits the disease to human beings.
A food-borne disease currently causing major concern in the United States, Canada, and Western Europe is caused by a particular variant of the common intestinal bacterium Escherichia coli, or E. coli for short. Although E. coli is normally present in the human intestines, the variant E. coli O157:H7 produces toxins that cause bloody diarrhea and, in some cases, far more severe problems, including kidney failure and death. A person can become infected by eating contaminated meat. Thorough cooking kills the bacteria.

A3. How the Body Fights Bacterial Disease

Our immune system is designed to protect us against harmful bacteria. It works to keep our normal microflora in check and also to eliminate invaders from outside the body. Some immune-system defenses are built in: The skin acts as a barrier to bacterial invaders, and antimicrobial substances in body secretions such as saliva and mucus can kill or stop the growth of some disease-causing bacteria. We acquire another immune-system defense through exposure to disease-causing bacteria.
After recovering from many bacterial infections, people have the ability to resist a second attack by the same bacteria. They can do so because their immune system forms disease-fighting proteins called antibodies designed to recognize specific bacteria. When next exposed to those bacteria, the antibodies bind to the surface of the bacteria and either kill them, prevent them from multiplying, or neutralize their toxin. Vaccines also can stimulate the immune system to form disease-fighting antibodies. Some vaccines contain strains of the bacterium that lack the ability to cause infection; others contain only parts of bacterial cells.

A4. Treatment and Prevention of Bacterial Disease
A4a. Antibiotics
In many cases the immune system can wipe out a bacterial infection on its own. But sometimes people become so sick from a bacterial disease that they require medical treatment. Antibiotics and other antibacterial drugs are the major weapons against disease-causing bacteria. Antibiotics act in a number of ways to kill bacteria or suppress their activity. Over time, however, bacteria can become resistant to antibiotics. As a result bacterial diseases have become more and more difficult to cure.
In an effort to control antibiotic resistance, physicians have tried to limit the use of antibiotics. In addition, they have advocated more vigorous efforts to improve the antibiotics we now have and to find new agents active against bacteria.

A4b. Vaccines
Immunization through vaccines is important in the prevention of infectious diseases caused by bacteria. Vaccines expose a human being or other animal to a disease-causing bacterium or its toxins without causing the disease. As a result of this exposure, the body forms antibodies to the specific bacterium. These antibodies remain ready to attack if they meet the bacteria in the future. Some immunizations last a lifetime, whereas others must be renewed with a booster shot.
Tetanus provides a good example of a successful vaccine. The bacterium Clostridium tetani, found in soil and ordinary dirt, produces one of the most lethal toxins known. The toxin affects nerves, resulting in muscle rigidity and death. Tetanus infection has become very rare in developed countries such as the United States where nearly everyone is immunized against the toxin. The vaccine immunizes the body by means of toxins that have been chemically treated so they are no longer toxic. Health officials recommend getting a tetanus shot every ten years. In less developed countries where vaccination is not so common, tetanus is a major cause of death, especially of babies.

A4c. Public Health Measures
Public health measures provide major controls against infectious disease. Especially important are those measures leading to ready availability of clean water, safe food, and up-to-date medical care. Waterborne diseases, such as cholera and typhoid fever, kill an estimated 5 million to 10 million people worldwide each year, according to the United Nations. Sufficient sources of clean drinking water in developing countries could help prevent these deaths. Food-safety guidelines can help prevent the spread of disease through contaminated food. Proper medical care can prevent transmission of infectious diseases to others. Tuberculosis, for example, kills more people worldwide every year than any other single disease. But if identified early, cases of tuberculosis can be treated effectively with antibiotics and other means, thereby stopping transmission to others.
Maintaining a clean environment for medical care is also important in preventing the spread of infectious diseases. For example, medical instruments, such as needles and syringes, must be sterile and proper infection-control procedures must be followed in hospitals, medical and dental offices, and industries that use bacteria. However, it is never possible, or even desirable, to have an environment entirely free of bacteria.

B. Bacteria and the Environment
Bacteria play a major role in recycling many chemical elements and chemical compounds in nature. Without such bacterial activities as the recycling of carbon dioxide (CO2) life on Earth would be impossible. Plants use CO2 to grow and in the process they produce the oxygen humans and other animals breathe. Moreover, we would drown in garbage and wastes if bacteria did not speed the decomposition of dead plant and animal matter.

B1. Nitrogen Fixation
Bacteria play a key role in making soil fertile. They convert nitrogen in Earth’s atmosphere into the nitrogen compound ammonia, which plants need to grow. Bacteria are the only organisms able to carry out this biochemical process known as nitrogen fixation. The bacteria able to fix atmospheric nitrogen usually live in association with plants, often integrated into the plant tissue. Bacteria in the genus Rhizobium, for example, form nodules (knobs) on the roots of beans and other plants in the legume family.

B2. The Carbon Cycle
Bacteria and fungi (yeasts and molds) are vital to another process that makes life on Earth possible: the carbon cycle. They help produce the gas carbon dioxide (CO2), which plants take from the atmosphere. During a part of the carbon cycle called photosynthesis, plants turn sunlight and CO2 into food and energy, releasing oxygen into the atmosphere.
The carbon cycle continues after plants and animals die, when bacteria help convert the material of which those organisms are made back into CO2. Bacteria and fungi secrete enzymes that partially break down dead matter. Final digestion of this matter takes place within bacterial and fungal cells by the processes of fermentation and respiration. The CO2 released by this action escapes back into the atmosphere to renew the cycle.

B3. Chemosynthesis
Bacteria are major players in cycles of other elements in the environment. Chemosynthetic bacteria use chemical energy, instead of the light energy used by plants, to change CO2 into something that other organisms can eat. Chemosynthesis occurs in vents at the bottom of the ocean, where light is unavailable for photosynthesis but hydrogen sulfide gas, H2S, bubbles up from below Earth’s crust. Life can develop around these vents because bacteria use the H2S in changing CO2 into organic nutrients. The H2S coming up from Earth’s mantle is extremely hot, but bacteria in these vent communities are adapted to the high temperatures. Bacteria’s ability to react chemically with sulfur compounds is useful in certain industrial processes as well.

B4. Bioremediation
Bioremediation refers to the use of microorganisms, especially bacteria, to return the elements in toxic chemicals to their natural cycles in nature. It may provide an inexpensive and effective method of environmental cleanup, which is one of the major challenges facing human society today.
Bioremediation has helped in cleaning up oil spills, pesticides, and other toxic materials. For example, accidents involving huge oil tankers regularly result in large spills that pollute coastlines and harm wildlife. Bacteria and other microorganisms can convert the toxic materials in crude oil to harmless products such as CO2. Adding fertilizers that contain nitrogen, phosphorus, and oxygen to the polluted areas promotes the multiplication of bacteria already present in the environment and speeds the cleanup process.

C. Bacteria in Agriculture and Industry
Many of bacteria’s beneficial roles in agriculture have been described in the previous section on Bacteria and the Environment. By recycling certain chemical elements and compounds, bacteria make plant and animal life possible. Bacteria’s chemical interactions have also found uses in industry. In recent decades, scientists have engineered bacterial genes to produce sought-after substances, such as human insulin, to use in the treatment of disease.

C1. Bacteria in Agriculture
Through the process of nitrogen fixation, bacteria turn nitrogen in the air into nutrients that crops and other plants need to grow. Some of the nitrogen-fixing bacteria attach to the roots of plants. Through the carbon cycle, bacteria produce the carbon dioxide that plants require for photosynthesis. Bacteria that live in the stomachs of cud-chewing animals, such as cows and sheep, help the animals digest grasses.
Bacteria also can be harmful in agriculture because of the major diseases of farm animals they cause. Many of the bacteria that cause infectious diseases in farm animals resemble those that cause similar human diseases. For example, a variant of the bacterium that causes human tuberculosis causes tuberculosis in cattle, and it can infect humans through cow’s milk. To prevent transmission of the disease, milk for human consumption should be pasteurized (heated at a temperature between 60° and 70°C (140° and 158°F) for a short time. Pasteurization kills most bacteria in milk.
Other disease-causing bacteria primarily affect animals other than humans. For example, the bacterium Brachyspira hyodysenteria causes a type of diarrhea in pigs that can be disastrous for pig farmers. Many infectious diseases of farm animals also affect wild animals, such as deer. Wild animals, in turn, can infect domestic animals, including cats and dogs.

C2. Bacteria in the Food Industry
Bacteria are of major importance in the food industry. On the one hand, they cause food spoilage and foodborne diseases, and so must be controlled. On the other hand, they improve food flavor and nutrition.
The dairy industry provides prime examples of bacteria’s harmful and helpful roles. Before the introduction of pasteurization in the late 1800s, dairy products were major carriers for bacteria that caused such illnesses as tuberculosis and rheumatic heart disease. Since that time regulation of the dairy industry has greatly reduced the risks of infection from dairy products.
On the helpful side, bacteria contribute to the fermentation (chemical breakdown) of many dairy products people eat every day. Yogurt, considered a healthful food, is produced by bacterial fermentation of milk. The bacteria produce lactic acid, which turns the milk sour, hampers the growth of disease-causing bacteria, and gives a desirable flavor to the resulting yogurt. Cheese also is produced by fermentation. First, bacteria ferment milk sugar to lactic acid. Then, cheese makers can introduce various microorganisms to produce the flavors they desire. The process is complicated and may take months or even years to complete, but it gives cheeses their characteristic flavors.
The variety of fermented foods we eat ranges from pickles, olives, and sauerkraut to sausages and other cured meats and fish, chocolate, soy sauce, and other products. In most of these fermentations, bacteria that produce lactic acid play major roles. Alcohol-producing yeasts are the primary fermentors in the manufacture of beer and wine, but lactic-acid bacteria also are involved, especially in making wine or cider. Bacteria that produce acetic acid can convert wine, cider, or other alcoholic beverages to vinegar.

C3. Bacteria in Waste Treatment
Bacteria are very important in sewage treatment. Standard sewage treatment involves multiple processes. It usually starts with settling during which large items sink to the bottom. Next, air is bubbled through the sewage. This so-called aerobic phase encourages oxygen-using bacteria to break down organic material in the sewage, such as human wastes, to acids and CO2. Most disease-causing organisms are also killed in this phase. The sewage sludge left behind is attacked in a subsequent phase by anaerobic bacteria (bacteria that cannot tolerate oxygen). These bacteria break down the sludge to produce methane gas, which can then be used as a fuel to power the treatment facility. In treatment plants today, this anaerobic phase sometimes precedes the aerobic phase.
Bacteria are also effective in cleaning up harmful wastes through bioremediation. In this process bacteria and other microorganisms convert toxic or otherwise objectionable wastes, such as pesticides and oil spills, to harmless or even useful products.

C4. Bacteria in Mineral Extraction
An interesting industrial process carried out by bacteria is the recovery of valuable minerals such as copper from ores. The most important copper ores are copper sulfides, which may contain only a small percentage of copper. Bacteria of the genera Thiobacillus and Sulfolobus are able to oxidize sulfides—that is, cause a chemical reaction of sulfides with oxygen—yielding sulfuric acid. This action produces the acid conditions necessary to leach (remove) the copper from the ores. The use of bacteria in extracting minerals, though slow, is environmentally friendly compared with the standard process of smelting. Smelting requires energy to heat the ore to extremely high temperatures for extracting minerals, and it also releases gases that pollute the air.
Some chemical reactions in which bacteria participate are harmful rather than helpful to industry. Bacteria are major agents of metal corrosion (wearing away) through the formation of rust, especially on metals containing iron. During the early stages of rust formation, hydrogen is produced, and it acts to slow the rusting process. However, certain bacteria use the hydrogen as a nutrient with the result that they greatly speed up rust formation.

C5. Bacteria in Biotechnology
Bacteria have been at the center of recent advances in biotechnology—the creation of products for human benefit through the manipulation of biological organisms. Biotechnology itself dates back at least as far as ancient Egyptian civilization. Paintings on the walls of Egyptian tombs depict the brewing of beer, which uses microorganisms in the fermentation process. However, the existence of bacteria did not become known until the development of sufficiently powerful microscopes in the late 1600s. During the centuries that followed, scientists became aware that living organisms were responsible for many biotechnological processes.
Biotechnology grew steadily during the 20th century. In the 1970s scientists used information about replication of viruses and bacteria and about DNA synthesis (manufacture) to begin the genetic engineering of bacterial cells. When scientists combined human DNA with the DNA in bacterial cells, recombinant DNA technology was born. Human DNA is the “recombinant.” DNA contains the instructions for creating proteins. With their recombinant DNA, bacteria became factories for turning out human proteins, such as the hormone insulin or antibodies that fight disease. Because they multiply so rapidly, bacteria produce multiple copies of proteins in a short time. The process of taking genetic information from one organism and placing it in a different organism was patented by American biochemists Stanley Cohen and Herbert Boyer in 1980. The genetic revolution was underway.

C6. Other Industrial Roles
Bacteria play a role in the production of other products, including certain plastics and enzymes used in laundry detergents. They also produce many antibiotics, such as streptomycin and tetracycline. Since the 1980s, bacteria have gained importance in the production of many bulk chemicals, including ethanol, a form of alcohol made from fermented corn. Ethanol is an ingredient of gasohol, a fuel that burns more cleanly than gasoline and uses less petroleum. Chemical production using bacteria and other microorganisms results in less pollution to the environment than standard chemical production. The growth of genetic engineering has opened the way to even greater use of bacteria in large-scale industrial manufacturing and environmentally friendly processes.

C7. Controlling Bacterial Growth
Sterilization and disinfection—processes for destroying microorganisms—are integral parts of the food industry. For example, canning involves heating foods to temperatures of 121oC (250oF) to kill all organisms, including the most heat-resistant bacterial cells. Failure to kill bacteria and the spores they produce can result in fatal disease such as botulism. If spores of the bacterium Clostridium botulinum are not destroyed, they can grow in canned foods and produce a toxin that attacks the nervous system. The botulism toxin is one of the most deadly toxins known.
Demand for better sterilization and disinfection methods in medicine and other industries has increased since the 1970s because of fear of spreading infection by the human immunodeficiency virus (HIV) and other disease-causing microorganisms. Industry has developed a wide array of products oriented to killing bacteria and other organisms. The industry has grown to be a huge one with a wide array of products oriented to killing bacteria and other microorganisms.


Bacteria are so small that they can be seen only under a microscope that magnifies them at least 500 times their actual size. Some become visible only at magnifications of 1,000 times. They are measured in micrometers (µm) and average about 1 to 2 µm in length. One micrometer equals one-millionth of a meter (0.0000001 m or about 0.000039 in).
Bacteria not only have many uses, they also occur in diverse shapes and types. As a group they carry out a broad range of activities and have different nutritional needs. They thrive in a variety of environments.

A. Types of Bacteria
Scientists use various systems for classifying bacteria into different types. One of the simplest systems is by shape. Other systems depend on oxygen use, source of carbon, and response to a particular dye.

A1. Classification by shape
Most bacteria come in one of three shapes: rod, sphere, or spiral. Rod-shaped bacteria are called bacilli. Spherical bacteria are called cocci, and spiral or corkscrew-shaped bacteria are called spirilla. Some bacteria come in more complex shapes. A hairlike form of spiral bacteria is called spirochete (see Spirochetes). Streptococci and staphylococci are well-known disease-causing bacteria among the cocci.

A2. Aerobic and Anaerobic Bacteria
Scientists also classify bacteria according to whether they need oxygen to survive or not. Aerobic bacteria require oxygen. Anaerobic bacteria cannot tolerate oxygen. Bacteria that live in deep ocean vents or within Earth are anaerobic. So are many of the bacteria that cause food poisoning.

A3. Autotrophic and Heterotrophic Bacteria
All bacteria require carbon for growth and reproduction. Bacteria called autotrophs (“self-feeders”) get their carbon from CO2. Most bacteria, however, are heterotrophs (“other feeders”) and derive carbon from organic nutrients such as sugar. Some heterotrophic bacteria survive as parasites, growing within another living cell and using the nutrients and cell machinery of their host cells. Some autotrophic bacteria, such as cyanobacteria, use sunlight to produce sugars from CO2. Others depend instead on energy from the breakdown of inorganic chemical compounds, such as nitrates and forms of sulfur.

A4. Gram-Positive and Gram-Negative Bacteria
Another system of classifying bacteria makes use of differences in the composition of cell walls. The difference becomes clear by means of a technique called Gram’s stain, which identifies bacteria as either gram-positive or gram-negative. After staining, gram-positive bacteria hold the dye and appear purple, while gram-negative bacteria release the dye and appear red. Gram-positive bacteria have thicker cell walls than gram-negative bacteria. Knowing whether a disease-causing bacterium is gram-positive or gram-negative helps a physician to prescribe the appropriate antibiotic. The stain is named for H. C. J. Gram, a Danish physician who invented it in 1884.

A5. The Cell and Its Structure
The cell wall generally determines the shape of the bacterial cell. The wall is a tough but resilient shell that keeps bacterial cells from drying out and helps them resist environmental stress. In some cases the cell wall protects the bacterium from attack by the body’s disease-fighting immune system cells. Some bacteria do not have much of a cell wall, while others have quite thick structures. Many species of bacteria move about by means of flagella, hairlike structures that project through the cell wall. The flagellum’s rotating motion propels the bacterial cell toward nutrients and away from harmful substances.
Like all cells bacteria contain the genetic material DNA. But bacterial DNA is not contained within a nucleus, as is DNA in plant and animal cells. Most bacteria have a single coil of DNA, although some bacteria have multiple pieces. Bacterial cells often have extra pieces of DNA called plasmids, which the cell may gain or lose without dying. Surrounding the DNA in a bacterial cell is cytoplasm, a watery fluid that is rich in proteins and other chemicals. A cell membrane inside the wall holds together the DNA and the constituents of the cytoplasm. Most activities of the bacterial cell are carried out within the cytoplasm, including nutrition, reproduction, and the manufacture of proteins.

B. How Bacteria Function
Bacterial cells, like all cells, require nutrients to carry out their work. These nutrients must be water soluble to enter through pores in the cell wall and pass through the cell membrane into the cytoplasm. Many bacteria, however, can digest solid food by secreting chemicals called exoenzymes into the surrounding environment. The exoenzymes help break down the solid food outside the bacteria into water-soluble pieces that the cell wall can absorb. Bacterial cells use nutrients for a variety of life-sustaining biochemical activities known collectively as metabolism.

B1. Anabolism and Catabolism
The metabolic activities that enable the cell to function occur in two ways: anabolism and catabolism. Simply put, anabolism is the manufacture of complex molecules from simple ones, and catabolism is the breakdown of complex molecules into simple ones. Cells use the energy from catabolism for all their other tasks, including growth, repair, and reproduction.
A single bacterial cell takes up small molecules from the environment by means of specific transport proteins in the cell membrane. In the case of more complex molecules, such as proteins or complex carbohydrates, bacteria first secrete digestive enzymes into the environment to break the nutrients down into smaller molecules, which are transported across the membrane. Enzymes (proteins that speed chemical reactions) within the cytoplasm then digest the molecules further. This breakdown, called catabolism, results in energy transfer through the processes of respiration and fermentation. During metabolism, some of the small molecules are converted into the molecules the cell needs to synthesize (manufacture) its own proteins, nucleic acids (building blocks of DNA), lipids (fatty substances), and polysaccharides (sugars and starches). The metabolic processes for synthesis of these complex cells are anabolism.

B2. Adaptation to Environmental Stress
All organisms have some capacity to adapt to environmental stress, but the extent of this adaptive capacity varies widely. Heat, cold, high pressure, and acid or alkaline conditions can all produce stress. Bacteria easily adapt to environmental stress, usually through changes in the enzymes and other proteins they produce. These adaptations enable bacteria to grow in a variety of conditions. Gradual exposure to the stress, for example, may enable bacteria to synthesize new enzymes that allow them to continue functioning under the stressing conditions or that enhance their capacity to deal with the stressing agent. Or they may resist environmental stress in other ways. Some bacteria that live in extremely acidic conditions can pump out acid from their cell.
Extremophiles are organisms that can grow in conditions considered harsh by humans. Some kinds of bacteria thrive in hydrothermal vents on the ocean floor or in oil reservoirs within Earth, at high pressures and temperatures as high as 120oC (250oF). Other kinds can live at temperatures as low as –12oC (10oF) in Antarctic brine pools. Other bacteria have adapted to grow in extremely acid conditions, where mines drain or minerals are leached from ores and sulfuric acid is produced. Others grow at extremely alkaline or extremely salty conditions. Still others can grow in the total absence of oxygen. Bacteria able to function in these extreme conditions generally cannot function under conditions we consider normal.

B3. Reproduction and Survival
Bacteria reproduce very rapidly. Replication in some kinds of bacteria takes only about 15 minutes under optimal conditions. One bacterial cell can become two in 15 minutes, four in 30 minutes, eight in 45 minutes, and so on. Bacteria would quickly cover the entire face of the globe if their supply of nutrients was unlimited. Fortunately for us, competition for nutrients limits their spread. In the absence of sufficient nutrients, however, many bacteria form dormant spores that survive until nutrients become available again. Spore formation also enables these bacteria to survive other harsh conditions.

B3a. Binary Fission
The simplest sort of bacterial reproduction is by binary fission (splitting in two). The bacterial cell first grows to about twice its initial size. Toward the end of that growth, the cell membrane forms a new membrane that extends inward toward the center of the cell. The cell wall follows closely behind, bisecting the cell. The membrane then seals to divide the enlarged cell into two small cells of equal or nearly equal size, and a new wall forms between the membranes.
The growth and division of a bacterial cell has two main phases. In one phase, the cell replicates its DNA and makes all the other molecules needed for the new cell. The second phase—cell division—occurs when DNA replication stops. In the bacterium E. coli replication takes about 40 minutes and cell division lasts about 20 minutes. The entire cycle takes about an hour. Yet the time for one cell to become two cells still takes only about 20 minutes. How is this possible? The cell does not wait for one cycle of replication to end before it starts another. Thus, a rapidly growing bacterial cell is carrying out multiple rounds of replication at the same time.

B3b. Spore Formation
In response to limited nutrients or other harsh conditions, many bacteria survive by forming spores that resist the environmental stress. Spores preserve the bacterial DNA and remain alive but inactive. When conditions improve, the spore germinates (starts growing) and the bacterium becomes active again.
The best-studied spores form within the bodies of Bacillus and Clostridium bacteria, and are known as endospores. Clostridium botulinum spores cause deadly botulism poisoning. Endospores have thick coverings and can resist environmental stress, especially heat. Even boiling in water does not readily kill them. But they can be killed by heating in a steel vessel filled with steam at high temperature and high pressure. Endospores can live for centuries in their dormant state.
Some bacteria form other types of spores. These spores are usually dormant but not as heat resistant or long-lived as endospores. Some aquatic bacteria, for example, attach to surfaces and produce swarmer cells during division. The swarmer cell swims away to attach to another surface and give rise to still more swarmer cells. Still other bacteria survive by forming colonies made up of millions of cells that act in a coordinated way to keep the organism alive.

B3c. Genetic Exchange
Bacterial cells often can survive by exchanging DNA with other organisms and acquiring new capacities, such as resistance to an antibiotic intended to kill them. The simplest method of DNA exchange is genetic transformation, a process by which bacterial cells take up foreign DNA from the environment and incorporate it into their own DNA. The DNA in the environment may come from dead cells. The more the DNA resembles the cell’s own DNA, the more readily it is incorporated.
Another means of genetic exchange is through incorporation of the DNA into a virus. When the virus infects a bacterial cell, it picks up part of the bacterial DNA. If the virus infects another cell, it carries with it DNA from the first organism. This method of DNA exchange is called transduction.
Transformation and transduction generally transfer only small amounts of DNA, although bacterial geneticists have worked to increase these amounts. Many bacteria are also capable of transferring large amounts of DNA, even the entire genome (set of genes), through physical contact. The donor cell generally makes a copy of the DNA during the transfer process so it is not killed. This method of exchange is called conjugation. DNA exchange enables bacteria that have developed antibiotic-resistant genes to rapidly spread their resistance to other bacteria.


Scientists long had difficulty classifying bacteria in relation to each other and in relation to other living things. Because bacteria are so small, scientists found it nearly impossible to identify characteristic structures on or in the organisms that would help in classification. For many years bacteria were considered to be plants and named according to the botanical system of classification, by genus and species. For example, Escherichia coli belongs to the genus Escherichia and to the species coli within that genus. The genus name starts with a capital letter; the species name, with a small letter. Both are written in italic letters. For convenience, people often use only the letter of the genus name, as in E. coli, for example.

A. A New Classification System
The development of the field of molecular phylogeny in the 1970s changed our view of bacteria. Phylogeny relates organisms through their evolutionary origins. In molecular phylogeny, scientists look for similarities in the molecules of organisms to figure out relationships. Initially, scientists looked at proteins, which are made up of long strings of amino acids. They figured that if a particular protein in two organisms contained exactly the same amino acids in the same order, then the two were very closely related or even identical. If there were only a few differences, the organisms were closely related. The more differences there were, the more distant the relationship would be.
Carl Woese, a microbiologist at the University of Illinois, discovered that it was easier to work with nucleic acids, such as DNA and RNA. He found that the best molecules were ribonucleic acid molecules from ribosomes (rRNA). Ribosomes are the biochemical machines inside cells that coordinate the synthesis of proteins. It was relatively easy to obtain rRNA, to identify its chemical building blocks known as nucleotides, and to determine the order of the nucleotides in the molecule. Because rRNA shows relatively little variation from one generation to the next, it proved to be an excellent tool for determining evolutionary relationships.
Molecular phylogeny indicated that there are three major groups, or kingdoms, of organisms. One kingdom, called Eukaryotae, consists of all organisms with a true nucleus and includes all plants and animals. The two other kingdoms, called Archaea and Eubacteria, consist of prokaryotic bacteria without a true nucleus. Archaea, or archaeabacteria, were once classified with other bacteria and the two kingdoms share many characteristics. Many of the archaea are extremophiles and can live in extremely hot, salty, or acid environments, but so can many eubacteria.
The classification of bacteria into two kingdoms, a system proposed by Woese, is based almost entirely on the structure of ribosomal RNA. But it appears to agree with other findings regarding the basic structures of the organisms, their metabolism, and their evolution.

B. Sequencing Bacterial DNA
Amazing advances in technology have enabled scientists to sequence the entire genome of many bacteria—that is, identify the nucleotides that make up the DNA and the order in which the nucleotides are arranged. This knowledge, and the sciences that have developed around it, will enable scientists to harness the useful capabilities of bacteria in agriculture, industry, and other fields and to develop new drugs. In one example, scientists have turned bacteria into factories for producing the hormone insulin by inserting human insulin-producing genes into bacteria. The insulin produced can be used to treat human diabetes.
Insulin is a protein, and genes govern the production of proteins by a cell. The study of protein production will help scientists understand the process of disease at a cellular level and help them develop new means of combating diseases. As scientists study how bacteria attach to and enter healthy cells, cause illness, and spread, they are learning useful details about the molecular structure of cells.


The oldest fossils of bacteria-like organisms date back as many as 3.5 billion years, making them the oldest-known fossils. These early bacteria could survive in the inhospitable conditions when Earth was young, extremely hot, and without oxygen. With the help of molecular phylogeny, scientists have pieced together a view of the evolution of bacteria. They believe that the kingdoms Archaea and Eubacteria had a common ancestor but separated very early on, a few billion years ago. Archaea may be the most common organisms on Earth today. Many of them can live without oxygen and without sunlight and inhabit such places as deep-sea vents. However, scientists currently know much more about the kingdom Eubacteria than the kingdom Archaea, because humans have more contact with disease-causing Eubacteria, such as streptococci and E. coli, and with Eubacteria such as lactobacilli used in food processing and other industries.
Over time, bacteria evolved to capture energy from the Sun’s light and thereby carry out the process of photosynthesis, converting sunlight into nutrients. Next they developed the sort of photosynthesis that plants today carry out by splitting water molecules to produce oxygen. With oxygen available, organisms that require it, such as animals, could inhabit Earth.
Recent discoveries suggest that Eukaryotae (plants and animals) probably evolved from Eubacteria. Many of the organelles (structures within the cytoplasm) of plant and animal cells are actually bacterial. Among organelles derived from bacteria that invaded plant or animal cells are mitochondria and chloroplasts. Mitochondria in plants and animals convert nutrients into energy-storage molecules. Chloroplasts house the photosynthetic machinery of plant cells. Not only do bacteria live on us and in us, but we ourselves are in a way partly bacterial.


Before the development of the microscope, some people speculated that small, invisible particles caused diseases and fermentations. But not until the late 1600s did anyone actually see bacteria. In the 1670s Dutch lens maker Antoni van Leeuwenhoek first saw what he called “wee animalcules” under his single-lens microscopes. Leeuwenhoek noticed cells of different shapes within a variety of specimens, including scrapings from his teeth and rainwater from gutters. His findings laid the foundation for the growth of microbiology.
The microscope was improved over the following centuries, but bacteria still appeared as tiny objects, even with magnifications of 1,000 times. In the 1930s, the first electron microscopes were developed. Using beams of electrons instead of light, these microscopes could magnify objects at least 200 times more than light microscopes could. With magnifications of 200,000 times actual size, it became possible to see structures within bacterial cells in detail.
Early studies of bacteria were difficult. In any environment many types of bacteria compete and cooperate, and all this activity makes it nearly impossible to figure out what each organism is doing. The first step was to separate different types of bacteria. One way of isolating bacteria was to grow them on a solid surface. Scientists first used kitchen foods, such as a potato slice cut with a sterile knife, on which to grow bacteria that attack plants. This method was not very convenient, however.
The perfect medium (environment) for growing bacteria also came from the kitchen, although its usefulness was demonstrated in the laboratory of German scientist Robert Koch. The medium was agar, a gel-forming substance that comes from seaweed. A coworker of Koch’s noted that his wife’s puddings remained solid in summer heat, whereas the gelatin on which he grew bacteria dissolved or got eaten by the bacteria. The firm puddings contained agar.
Agar dissolves in water only at temperatures close to boiling. When it cools, it forms a stable gel. Most bacteria cannot digest it. Bacteriologists could transfer a bacterial specimen onto a plate of agar using sterile wires or loops, and obtain a colony of organisms. If more than one type of bacteria formed a colony, the scientists could repeat the process, growing each type on a separate agar plate to obtain a pure culture (laboratory-grown specimen) for study. They could also add nutrients to agar to provide the bacteria with the food they need for growth. In addition, they could add substances to suppress the growth of unwanted bacteria but not the growth of those the bacteriologist wished to isolate. Growing bacteria on agar has become routine in laboratories.
Bacteriologists have become accustomed to studying individual types of bacteria in pure cultures. In nature, however, bacteria usually live in diverse communities, often with hundreds of types of organisms. These communities form sticky masses called biofilms on soil particles, ocean debris, plants and animals, and just about any solid or liquid surface. In our bodies, biofilms develop on teeth, on the soft tissues of the mouth and throat, on the membrane lining the nose and sinuses, in the gut, and on all other exposed body surfaces. In nature, organisms form microbial mats on surfaces between water and air. In sewage treatment, bacteria clump together in masses. All these communities are highly diverse, harboring many kinds of organisms. They can be compared to cities in which the different members have different functions, all important to maintaining the community.
Bacteriologists are realizing more and more the need to move from studying pure cultures containing only a single species to the study of communities in biofilms and microbial mats. The growth of molecular biology and the capacity to study bacteria in molecular detail have demonstrated that the bacterial world is far more diverse than previously thought. It seems possible that we currently have discovered only a small fraction of existing types of bacteria in the world. Perhaps as many as 95 percent of total types remain unknown.
Scientists have already sequenced the entire genome for many bacteria. Researchers can cut pieces from bacterial DNA and replicate it in many copies. Through DNA transfer, the pieces can be inserted in bacterial cells. The cells with the new DNA may then start to make new proteins they were unable to make previously. Thus, bacteria can be genetically engineered to make a whole range of products and to develop new functions. Genetic engineering has opened up a new world of biology and a tremendous opportunity to explore bacteria and other microorganisms and to benefit humanity from the resulting knowledge.

Contributed By:
Robert E. Marquis


Cyanobacteria or Blue-Green Algae, members of a group of photosynthetic prokaryotes single-celled organisms that lack an enclosed nucleus and other specialized cell structures. Like green plants, cyanobacteria contain chlorophyll but the chlorophyll is not located in chloroplasts; rather it is found in chromatophores, infoldings of the plasma membrane where photosynthesis is carried out. In many species, other pigments mask the chlorophyll and impart a bluish or sometimes reddish color. Some species are free-living, but most aggregate in colonies or form filaments. Reproduction is by simple cell division or by fragmentation of the filaments.
Cyanobacteria are found throughout the world in diverse habitats. They are abundant on tree bark and rocks and in moist soil, where they carry on nitrogen fixation. Some symbiotically coexist with fungi to form a lichen. In hot weather some species form large and occasionally toxic blooms on the surfaces of ponds and coastal waters. In shallow tropical waters, mats of the cyanobacteria grow into humps called stromatolites. Fossil stromatolites are found in rocks formed more than 3 billion years ago, during Precambrian time. They suggest that cyanobacteria played a role in changing the ancient carbon dioxide-rich atmosphere into the oxygenated mixture that exists today.
Scientific classification: Cyanobacteria make up the phylum Cyanophyta, in the kingdom Prokaryotae.

Microsoft ® Encarta ® 2006. © 1993-2005 Microsoft Corporation. All rights reserved.

Senin, 30 Juni 2008

About Biology Science

1.1 The Process of Science

The statements made by Jake’s friends and family about what actions will help him remain healthy (for example, his mother’s advice to wear a hat) are in some part based on the advice-giver’s understanding of how our bodies resist colds.
Ideas about “how things work” are called hypotheses. Or, more formally, a hypothesis is a proposed explanation for one or more observations. All of us generate hypotheses about the causes of some phenomenon based on our understanding of the world (Figure 1.1). When Jake’s mom tells him to dress warmly in order to avoid colds, she is basing her advice on her belief in the fol lowing hypothesis: Becoming chilled makes an individual more susceptible to becoming ill.
The hallmark of science is that hypotheses are subject to rigorous testing. Therefore, scientific hypotheses must be testable—it must be possible to evaluate the hypothesis through observations of the measurable universe. Not all hypotheses are testable. For instance, the statement that “colds are generated by disturbances in psychic energy” is not a scientific hypothesis, since psychic energy cannot be seen or measured—it does not have a material nature. In addition, hypotheses that require the intervention of a supernatural force cannot be tested scientifically. If something is supernatural, it is not constrained by the laws of nature, and its behavior cannot be predicted using our current understanding of the natural world.
Scientific hypotheses must also be falsifiable, that is, able to be proved false. The hypothesis that exposure to cold temperatures increases your susceptibility to colds is falsifiable, because we can imagine an observation would cause us to reject this hypothesis (for instance, the observation that people exposed to cold temperatures do notcatch more colds than people protected fromchills). However, hypotheses that are judgments, such as “It is wrong to cheat on an exam,” are not scientific, since different people have different ideas about right and wrong. It is impossible to falsify these types of statements.
The Logic of Hypothesis Testing Of all the advice Jake has heard, he is inclined toward that given by his lab partner. She insisted that taking vitamin C supplements was keeping her healthy. Jake also recalls learning about vitamin C in his Human Nutrition class last year. In particular, he remembers that:
1. Fruits and vegetables contain lots of vitamin C.
2. People with diets rich in fruits and vegetables are generally healthier than people who skimp on these food items.
3. Vitamin C is known to be an anti-inflammatory agent, reducing throat and nose irritation.
Given his lab partner’s experience and what he learned in class, Jake makes the following hypothesis:
Consuming vitamin C decreases the risk of catching a cold. This hypothesis makes sense. After all, Jake’s lab partner is healthy and Jake has made a logical case for why vitamin C is good cold prevention. This certainly seems like enough information on which to base his decision about how to proceed—he should start taking vitamin C supplements if he wants to avoid future colds. However, a word of caution: Just because a hypothesis seems logical does not mean that it is true. Consider the ancient hypothesis that the sun revolves around Earth, asserted by Aristotle in approximately 350 B.C.This hypothesis was logical, based on the observation that the sun appeared on the eastern horizon every day at sunrise and disappeared behind the western horizon at sunset. For two thousand years, this hypothesis was considered to be “a fact” by nearly all of Western society. To most people, the hypothesis made perfect sense, especially since the common religious belief in Western Europe was that Earth had been created and then surrounded by the vault of heaven. It was not until the early seventeenth century that this hypothesis was falsified as the result of observations made by Galileo Galilei of the movements of Venus. Galileo’s work helped to confirm Nicolai Copernicus’ more modern hypothesis that Earth revolves around the sun. So even though Jake’s hypothesis about vitamin C is perfectly logical, it
needs to be tested. Hypothesis testing is based on a process called deductive reasoningor deduction. Deduction involves making a specific predictionabout the outcome of an action or test based on observable facts. The prediction is the result we would expect from a particular test of the hypothesis.
Deductive reasoning takes the form of “if/then” statements. Aprediction based on the vitamin C hypothesis could be:
If vitamin C decreases the risk of catching a cold, then people who take vitamin C supplements with their regular diets will experience fewer colds than people who do not take supplements.
Deductive reasoning, with its resulting predictions, is a powerful method for testing hypotheses. However, the structure of such a statement means that hypotheses can be clearly rejected if untrue, but impossible to prove if they are true (Figure1.2). This shortcoming is illustrated using the “if/then” statement above. Consider the possible outcomes of a comparison between people who supplement with vitamin C and those who do not: People who take vitamin C supplements may suffer through more colds than people who do not, they may have the same number of colds as people who do not supplement, or supplementers may in fact experience fewer colds. What do these results tell Jake about his hypothesis?
If people who take vitamin C have more colds, or the same number of colds as those who do not supplement, the hypothesis that vitamin C alone provides protection against colds can be rejected. But what if people who supplement with vitamin C doexperience fewer colds? If this is the case, should Jake be out proclaiming the news, “Vitamin C—A Wonder Drug that Prevents the Common Cold”? No, he should not. Jake needs to be much more cautious than that; he can only say that he has supported and not disproven the hypothesis.
Why is it impossible to say that the hypothesis that vitamin C prevents colds is true? Primarily because there could be other factors (that is, there are alternative hypotheses) that explain why people with different vitamin-taking habits are different in their cold susceptibility. In other words, demonstrating the truth of the thenportion of a deductive statement does not guarantee that the if portion is true.
Consider the alternative hypothesis that frequent exercise reduces susceptibility to catching a cold. Perhaps people who take vitamin C supplements are more likely to engage in regular exercise than those who do not supplement. What if the alternative hypothesis were true? If so, the prediction that people who take vitamin C supplements experience fewer colds than people who do not supplement would be true, but not because the original hypothesis (vitamin C reduces the risk of cold) is true. Instead, people who take vitamin C supplements experience fewer colds than people who do not supplement because they are more likely to exercise, and it is exercise that reduces cold susceptibility.