H-Evolution-004Prokaryotes

Prokaryotes

The history of prokaryotic life is a success story spanning billions of years (Figure 15.8). Prokaryotes lived and evolved all alone on Earth for 2 billion years. They have continued to adapt and flourish on an evolving Earth and in turn have helped to change Earth.

They're Everywhere!

Today, prokaryotes are found wherever there is life, and they outnumber all eukaryotes combined. More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than the total number of people who have ever lived. Prokaryotes also thrive in habitats too cold, too hot, too salty, too acidic, or too alkaline for any eukaryote. In 1999, biologists even discovered prokaryotes growing on the walls of a gold mine 2 miles below Earth's surface.

Figure 15.8a Figure 15.8b Figure 14.27

Figure 15.8 Over 3 billion years of prokaryotes. (a) This microscopic fossil is a filamentous species consisting of a chain of prokaryotic cells. It is one of a diversity of prokaryotes found in western Australian rocks that are about 3.5 billion years old. (b) The orange rods are individual modern bacteria, each about 5 mm long, on the head of a pin. Most prokaryotic cells have diameters in the range of 1-10 mm, much smaller than most eukaryotic cells (typically 10-100 mm). This micrograph will help you understand why a pin prick can cause infection. And it will help you remember to flame the tip of a needle before using it to remover a splinter. The heat kills the bacteria.

Though individual prokaryotes are relatively small organisms, they are , giants in their collective impact on Earth and its life. We hear most about a few species that cause serious illness. During the fourteenth century, Black Death-bubonic plague, a bacterial disease-spread across Europe, killing an estimated 25% of the human population. Tuberculosis; cholera, many sexually transmissible diseases, and certain types of food poisoning are some other human diseases caused by bacteria.

However, prokaryoric life is no rogue’s gallery. Far more common than harmful bacteria are those that are benign or beneficial. Bacteria in our intestines provide us with important vitamins, and others living in our mouth prevent harmful fungi from growing there. Prokaryotes also recycle carbon and other vital chemical elements back and forth between organic matter and the soil and atmosphere. For example, there are prokaryotes that decompose dead organisms. Found in soil and at the bottom of lakes, rivers, and oceans, these decomposers return chemical elements to the environment in the form of inorganic compounds that can be used by plants, which in turn feed animals. If prokaryotic decomposers were to disappear, the chemical cycles that sustain life would come to a halt. All forms of eukaryotic life would also be doomed. In contrast, prokaryotic life would undoubtedly persist in the absence of eukaryotes, as it once did for 2 billion years.

The Two Main Branches of Prokaryotic Evolution: Bacteria and Archaea

Prokaryotes have a cellular organization fundamentally different from that of eukaryotes. Whereas eukaryotic cells have a membrane-enclosed nucleus and numerous other membrane-enclosed organelles, prokaryotic cells lack these structural features. The traditional five-kingdom classification scheme emphasizes this fundamental difference in cellular organization. Prokaryotes make up the kingdom Monera, separate from the four eukaryotic kingdoms (Protista, Plantae, Fungi, and Animalia). In the past two decades, however, researchers have learned that a single prokaryotic kingdom may not fit evolutionary history. By comparing genomes of diverse prokaryotes, biologists have identified two major branches of prokaryotic evolution: the bacteria and the archaea. Though they have prokaryotic cell organization in common, bacteria and cuchaea differ in many structural, biochemical, and physiological characteristics. And there is also evidence that archaea are more closely related to eukaryotes than they are to bacteria. It was these discoveries that prompted the three-domain classification- domains Bacteria, Archaea, and Eukarya - which you can review in Figure 14.27b. The majority of prokaryotes are bacteria, but the archaea are worth studying for their evolutionary and ecological significance.

The term archaea ("ancient") refers to the antiquity of the group's origin from the earliest cells. Even today, most species of archaea inhabit extreme environments, such as hot springs and salt ponds. Few other modem organisms (if any) can survive in these environments, which may resemble habitats on the early Earth.

Biologists refer to some archaea as "extremophiles:' meaning "lovers of the extreme:' There are extreme halophiles ("salt lovers"), archaea that thrive in such environments as Utah's Great Salt Lake and seawater-evaporating ponds used to produce salt (Figure 15.9) .There are also extreme thermophiles ("heat lovers") that live in very hot water; some even populate the deep-ocean vents that gush superheated water hotter than 100°C, the boiling point of water at sea level. And then there are the methanogens, archathat live in anaerobic environments and give off methane as a waste product. They are abundant in the anaerobic mud at the bottom of lakes and swamps. You may have seen methane, also called marsh gas, bubbling up from a swamp. Great numbers of methanogens also inhabit the digestive tracts of animals. In humans, intestinal gas is largely the result of their metabolism. More importantly, methanogens aid digestion in cattle, deer, and other animals that depend heavily on cellulose for their nutrition. Normally, bloating does not occur because these animals regularly belch out large volumes of gas produced by the methanogens and other microorganisms that enable them to utilize cellulose. And that may be more than you wanted to know about these gas-producing microbes.

Figure 15.9 Figure 4.5 Prokaryote

Figure 15.9 Extreme halophiles (“salt-loving” archaea). These are seawater-evaporating ponds at the edge San Francisco Bay. The colors of the ponds result from dense growth of the prokaryotes that thrive when the salinity of the water reaches 15-20% (before evaporation, seawater has a salt concentration of about 3%). The ponds are used for commercial salt production; the halophilic archaea are harmless.

Figure 15.10 Figure 15.11

Figure 15.11 Some examples of bacterial diversity (a) This prokaryotic organism, called an actinomycete, is a mass of branching chains of rod-shaped cells. These bacteria are very common in soil, where they break down organic substances. The filaments enable the organism to bridge dry gaps between soil particles. Most species secrete antibiotics, which inhibit the growth of competing bacteria. Pharmaceutical companies use various species of actinomycetes to produce antibiotic drugs, including streptomycin. (b) This filamentous prokaryote belongs to a photosynthetic group called the cyanobacteria. Many species are truly multicellular in having a division of labor among specialized cells. The box on this micrograph highlights a cell that converts atmospheric nitrogen to ammonia, which can then be incorporated into amino acids and other organic compounds. (c) There are actually some prokaryotic cells that are gigantic, even by eukaryoti standards. The bright ball in this photo is a marine bacterium discovered in 1997 (the two smaller spheres above it are dead cells) This prokaryotic cell is over half a millimeter in diameter, about the size of a fruit fly's head.

The Structure, Function, and Reproduction of Prokaryotes

You can use Figure 4.5 to review the general structure of prokaryotic cells. Note again the absence of a true nucleus and the other membrane-enclosed organelles characteristic of the much more complex eukaryotic cells. Another feature to note in prokaryotes is that nearly all species have cell walls exterior to their plasma membranes. These walls are chemically different from the cellulose walls of plant cells. Some antibiotics, including the penicillins, kill certain bacteria by incapacitating an enzyme the microbes use to make their walls. Determining cell shape by microscopic examination is an important step in identifying prokaryotes (Figure 15.10). Spherical species are called cocci (singular, coccus), from the Greek word for "berries." Cocci that occur in clusters are called staphylococci ("cluster of grapes"), or staph for short (as in "staph infections"). Other cocci occur in chains; they are called I streptococci ("twisted grapes"). The bacterium that causes strep throat in humans is a streptococcus. Rod-shaped prokaryotes are called bacilli (singular, bacillus). A third group of prokaryotes are curved or spiral-shaped. The largest spiral-shaped prokaryotes are called spirochetes. The bacterium that causes syphilis, for example, is a spirochete. The culprit that causes Lyme disease is also a spirochete. Most prokaryotes are unicellular and very small, but there are exceptions to both of these generalizations. Some species tend to aggregate transiently into groups of two or more cells, such as the streptococci already mentioned. Others form true colonies, which are permanent aggregates of identical cells (Figure 15.11a). And some species even exhibit a simple multi cellular organization, with a division of labor between specialized types of cells (Figure 15.11 b ). Among unicellular species, there are some giants that actually dwarf most eukaryotic cells (Figure 15.11 c).

Figure 15.12 Figure 15.13

Figure 15.12 Prokaryotic flagella. These locomotor appendages are entirely different in structure and mechanics from the eukaryotic flagella discussed in Chapter 4. At the base of the prokaryotic version is a motor and set of rings embedded in the plasma membrane and cell wall. This machinery actually spins like a wheel, rotating the filament of the flagellum.

Figure 15.13 An anthrax endospore. This prokaryote is Bacillus anthracis, the notorious bacterium that produces the deadly disease called anthrax in cattle, sheep, and humans. There are actually two cells here, one inside the other. The outer cell produced the specialized inner cell, called an endospore. The endospore has a thick, protective coat. Its cytoplasm is dehydrated, and the cell does not metabolize. Under harsh conditions, the outer cell may disintegrate, but the endospore survives all sorts of trauma, including lack of water and nutrients, extreme heat or cold, and most poisons. When the environment becomes more hospitable, the endospore absorbs water and resumes growth. In late 2001, one or more bioterrorists disseminated anthrax spores through the U.S. postal system.

About half of all prokaryotic species are motile. Many of those travelers have one or more flagella that propel the cells away from unfavorable places or toward more favorable places, such as nutrient-rich locales (Figure 15.12).

Although few bacteria can thrive in the extreme environments favored by many archaea, some bacteria can survive extended periods of very harsh conditions by forming specialized "resting" cells, or endospores (Figure 15.13) .Some endospores can remain dormant for centuries. Not even boiling water kills most of these resistant cells. To sterilize laboratory equipment, microbiologists use an appliance called an autoclave, a pressure cooker that kills endospores by heating to a temperature of 121°C (250°F) with high-pressure steam. The food-canning industry uses similar methods to kill endospores of dangerous soil bacteria such as Clostridium botulinum, which produces a toxin that causes the potentially fatal disease botulism.

Most prokaryotes can reproduce at a phenomenal rate if conditions are favorable. The cells copy their DNA almost continuously and divide again and again by the process called binary fission. To understand how this makes explosive population growth possible, flash back to that childhood numbers game: "Would you rather have a million dollars or start out with just a penny and have it doubled every day for a month?" If you opt for the penny, you feel like a loser at midmonth, when you have only a few hundred dollars. But by the end of the month, you've bagged about 10 million bucks. This is the exponential growth that repeated doublings make possible. Now apply that concept to bacterial reproduction, except double the number every 20 minutes. That's the rate at which some bacteria can divide if there is plenty of food and space. In just 24 hours, a single tiny cell could give rise to a bacterial colony equivalent in mass to about 15,000 humans! Fortunately, few bacterial populations can sustain exponential growth for long. Environments are usually limiting in resources such as food and space. The bacteria also produce metabolic waste products that may eventually pollute the colony's environment. Still, you can understand why certain bacteria can make you sick so soon after just a few cells infect you - or why food can spoil so rapidly. Refrigeration retards food spoilage not because the cold kills the bacteria on food but because most microorganisms reproduce only very slowly at such low temperatures.

The Nutritional Diversity of Prokaryotes

Prokaryotic evolution "invented" every type of nutrition we observe through out life, plus some nutritional modes unique to prokaryotes. Nutrition refers here to how an organism obtains two resources for synthesizing organic compounds: energy and a source of carbon. Species that use light energy are termed phototrophs. Chemotrophs obtain their energy from chemicals taken from the environment. If an organism needs only the inorganic compound carbon dioxide (CO₂) as a carbon source, it is called an autotroph. Heterotrophs require at least one organic nutrient - the sugar glucose, for instance - as a source of carbon for making other organic compounds. We can combine the phototroph-versus-cheniotroph (energy source) and autotroph-versus-heterotroph (carbon source) criteria to group organisms according to four major modes of nutrition:

1. Photoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from CO₂. Among the diverse groups of photosynthetic prokaryotes are the cyanobacteria, such as the species in Figure 15.11 b. All photosynthetic eukaryotes-plants and algae-also fit into this nutritional. category.

2. Chemoautotrophs need only CO₂ as a carbon source. However, instead of using light for energy, these prokaryotes extract energy from certain inorganic substances, such as hydrogen sulfide (H₂S) or ammonia (NH₃). This mode of nutrition is unique to certain prokaryotes. For example, prokaryotic species living around the hot-water vents deep in the seas are the main food producers in those bizarre ecosystems.

3. Photoheterotrophs can use light to generate ATP but must obtain their carbon in organic form. This mode of nutrition is restricted to certain prokaryotes.

4. Chemoheterotrophs must consume organic molecules for both energy and carbon. This nutritional mode is found widely among prokaryotes, certain protists, and even some plants. And all fungi and animals are chemoheterotrophs.

Table 15.1 reviews the four major modes of nutrition.

Table 15.1	Nutritional Classification of Organisms
Nutritional Type	Energy Source	Carbon Source
Photoautotroph (photosynthesizer)	Sunlight	CO2
Chemoautotroph	Inorganic chemicals,	CO2
Photoheterotroph	Sunlight	Organic compounds
Chemoheterotroph	Organic compounds	Organic compounds

Figure 15.14 Really bad bacteria. The yellow rods are Haemophilus influenzae bacteria on skin cells lining the interior of a human nose. These pathogens are transmitted through the air. H. influenzae, not to be confused with influenza (flu) viruses, causes pneumonia and other lung infections that kill about 4 million people worldwide per year. Most victims are children in developing countries, where malnutrition lowers resistance to all pathogens.

The Ecological Impact of Prokaryotes

Organisms as pervasive, abundant, and diverse as prokaryotes are guaranteed to have tremendous impact on Earth and all its inhabitants. Here we survey just a few examples of prokaryotic clout.

Bacteria That Cause Disease We are constantly exposed to bacteria, some of which are potentially harmful (Figure 15.14). Bacteria and other microorganisms that cause disease are called pathogens. Most of us are healthy most of the time only because our body defenses check the growth of pathogens. Occasionally, the balance shifts in favor of a pathogen, and we become ill. Even some of the bacteria that are normal residents of the human body can make us sick when our defenses have been weakened by poor nutrition or by a viral infection.

Most pathogenic bacteria cause disease by producing poisons. There are two classes of these poisons: exotoxins and endotoxins. Exotoxins are poisonous proteins secreted by bacterial cells. A single gram of the exotoxin that causes botulism could kill a million people. Another exotoxin producer is Staphylococcus aureus (abbreviated S. aureus). It is a common, usually harmless resident of our skin surface. However, if S. aureus enters the body through a cut or other wound or is swallowed in contaminated food, it can cause serious diseases. One type of S. aureus produces exotoxins that cause layers of skin to slough off; another can cause vomiting and severe diarrhea; yet another can produce the potentially deadly toxic shock syndrome. In contrast to exotoxins, endotoxins are not cell secretions but are chemical components of the cell walls of certain bacteria. All endotoxins induce the same general symptoms: fever, aches, and sometimes a dangerous drop in blood pressure (shock). The severity of symptoms varies with the host's condition and with the bacterium. Different species of Salmonella, for example, produce endotoxins that cause food poisoning and typhoid fever.

During the last 100 years, following the nineteenth-century discovery that "germs" cause disease, the incidence of bacterial infections has declined, particularly in developed nations. Sanitation is generally the most effective way to prevent bacterial disease. The installation of water treatment and sewage systems continues to be a public health priority through-out the world. Antibiotics have been discovered that can cure most bacterial diseases. However, resistance to widely used antibiotics has evolved in many of these pathogens.

In addition to sanitation and antibiotics, a third defense against bacterial disease is education. A case in point is Lyme disease, currently the most widespread pest-carried disease in the United States. The disease is caused by a spirochete bacterium carried by ticks that live on deer and field mice (Figure 15.15) .Lyme disease usually starts as a red rash shaped like a bull's-eye around a tick bite. Antibiotics can cure the disease if administered within about a month after exposure. If untreated, Lyme disease can cause debilitating arthritis, heart disease, and nervous disorders. A vaccine is now available, but it does not give full protection. The best defense is public education about avoiding tick bites and the importance of seeking treatment if a rash develops. When walking through brush, using insect repellent and wearing light-colored clothing can reduce contact with ticks.

Pathogenic bacteria are in the minority among prokaryotes. Far more common are species that are essential to our well-being, either directly or indirectly. Let's turn our attention now to the vital role that prokaryotes play in sustaining the biosphere.

Prokaryotes and Chemical Recycling Not too long ago, in geologic terms, the atoms of the organic molecules in your body were parts of the in-organic compounds of soil, air, and water, as they will be again. Life depends on the recycling of chemical elements between the biological and physical components of ecosystems. Prokaryotes play essential roles in these chemical cycles. For example, cyanobacteria not only restore oxygen to the atmosphere; some of them also convert nitrogen gas (N₂) in the atmosphere to nitrogen compounds that plants can absorb from soil and water (see Figure 15.11 b ). Other prokaryotes, including bacteria living within the roots of bean plants and other legumes, also contribute large amounts of nitrogen compounds to soil. In fact, all the nitrogen that plants use to make proteins and nucleic acids comes from prokaryotic metabolism in the soil, In turn, animals get their nitrogen compounds from plants.

Another vital function of prokaryotes is the breakdown of organic waste and dead organisms. Prokaryotes decompose organic matter and, in the process, return elements to the environment in inorganic forms that can be used by other organisms. If it were not for such decomposers, carbon, nitrogen, and other elements essential to life would become locked in the organic molecules of corpses and waste products.

Prokaryotes and Bioremediation Humans have put the metabolically divers prokaryotes to work in cleaning up the environment. The use of organisms to remove pollutants from water, air, and soil is called bioremediation. The most familiar example of bioremediation is the use of prokaryotic decomposers to treat our sewage. Raw sewage is first passed through a series of screens and shredders, and solid matter is allowed to settle out from the liquid waste. This solid matter, called sludge, is then gradually added to a culture of anaerobic prokaryotes, including both bacteria and archaea. The microbes decompose the organic matter in the sludge, converting it to material that can be used as landfill or fertilizer after chemical sterilization. Liquid wastes are treated separately from the sludge Figure 15.16).

We are just beginning to explore the great potential that prokaryotes offer for bioremediation. Certain bacteria that occur naturally on ocean beaches can decompose petroleum and are useful in cleaning up oil spills (Figure 15.17). Genetically engineered bacteria may be able to degrade oil more rapidly than the naturally occurring oil-eaters. Bacteria may also help us clean up old mining sites. The water that drains from mines is highly acidic and is also laced with poisons-often compounds of arsenic, copper, zinc, and the heavy metals lead, mercury, and cadmium. Contamination of our soils and groundwater by these toxic substances poses a widespread threat, and cleaning up the mess is extremely expensive. Although there are no simple solutions to the problem, prokaryotes may be able to help. Bacteria called Thiobacillus thrive in the acidic waters that drain from mines. Some mining companies use these microbes to extract copper and other valuable metals from low-grade ores. While obtaining energy by oxidizing sulfur or sulfur- containing compounds, the bacteria also accumulate metals from the mine waters. Unfortunately, their use in cleaning up mine wastes is limited be- cause their metabolism also adds sulfuric acid to the water. If this problem is solved, perhaps through genetic engineering, Thiobacillus and other prokaryotes may help us overcome some environmental dilemmas that seem intractable today. One current research focus is a bacterium that tolerates radiation doses thousands of times stronger than those that would kill people. This species may help clean up toxic dump sites that include radioactive wastes.

Figure 15.16 Figure 15.17

Figure 15.16 Putting prokaryotes to work in sewage treatment facilities. This is a trickling filter system, one type of mechanism for treating liquid wastes after sludge is removed. The long horizontal pipes rotate slowly, spraying liquid wastes through the air onto a thick bed of rocks. Bacteria and fungi growing on the rocks remove much of the organic material dissolved in the waste. Outflow from the rock bed is sterilized and then released, usually into a river or ocean.

Figure 15.17 Treatment of an oil spill in Alaska. The workers are spraying fertilizers onto an oil-soaked beach. The fertilizers stimulate growth of naturally occurring bacteria that initiate the breakdown of the oil. This technique is the fastest and least expensive way yet devised to clean up spills on beaches. Of course, it would be much better to keep oil off the beaches in the first place!

It is the nutritional diversity of prokaryotes that makes such benefits as chemical recycling and bioremediation possible. 'The various modes of nutrition and metabolic pathways we find throughout life are all variations on themes that prokaryotes "invented" during their long reign as Earth's exclusive inhabitants. Prokaryotes are at the foundation of life in both the ecological sense and the evolutionary sense. The subsequent breakthroughs in evolution were mostly structural, including the origin of the eukaryotic cell and the diversification of the organisms we call protists.