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CH A P T ER 4

PROKARYOTES—BACTERIA AND ARCHAEA

Within one linear centimeter of your lower colon there lives and works more bacteria (about 100 billion) than all humans who have ever been born. Yet many people continue to assert that it is we who are in charge of the world.

—Neil DeGrasse Tyson

Introduction

Half or more of the “living protoplasm” on Earth is microscopic. The majority of these tiny beings are bacteria and archaea. Biologists estimate (guesstimate) the total number of bacteria and archaea at over 3 X 1030 or 3 nonillion. Estimating the number of bacterial species is just as much a guess

as determining the number of total bacterial cells with estimates ranging anywhere from 100,000 species to 10 million species. To study bacteria, you don’t have to go far because your own body is a bacterial biosphere unto itself.

The human body contains about 100 trillion cells, but only maybe one in 10 of those cells are actu-ally—human. The rest are archaea, bacteria, viruses and other microorganisms. These microbes aren’t just along for the ride. They’re there for a reason. We have a symbiotic relationship with them in that we give them a place to live, and they help keep us alive. They belong in and on our bodies; they help support our

ORGANISMS AND ECOLOGY

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health; they help digest our food and provide many kinds of protective mechanisms for human health. The next time you look in the mirror consider that what you see is more microbe than human.

History of Prokaryotes

Today biologists recognize three main branches on the tree of life. These branches, known as domains, are Archaea, Bacteria, and Eukaryota. The single-celled Archaea and Bacteria are deemed prokaryotes because their cells have nuclei not contained within a membrane and they lack organelles. The mostly multicellular members of Eukaryota are designated as eukaryotes because their cells have a membrane-bound nucleus and numerous complex organelles.

The archaea were once considered to be an unusual group of bacteria and so were named archaebacte-ria. However, it is now known that Archaeans have an independent evolutionary history and have numerous differences in the biochemistry compared to that of other forms of life. The differences are so great that they are now classified as a distinctly separate domain in the three-domain system. If you were shrunk to their size, bacteria and archaea would seem to you as different from each other as insects and fish.

Prokaryotes are possibly the most ancient form of life. Fossils purported to be prokaryote cells in stro-matolites have been dated to almost 3.5 billion years old, and the remains of lipids that may be prokaryotes have been detected in shales dating from 2.7 billion years ago. Since most prokaryotes do not have distinct morphologies, the shape of fossils cannot be used to identify them. Instead, chemical fossils in the form of unique isoprene lipids found in prokaryotes are used. The oldest known traces of lipids have been found in Greenland in sediments formed 3.8 billion years ago. However, some scientists dispute this claim.

The early Earth was hot, with a lot of extremely active volcanoes and an atmosphere composed mostly of nitrogen, methane, ammonia, carbon dioxide, and water. There was little if any oxygen in the atmosphere. Archaea and some bacteria evolved in these conditions, and can live in similar harsh conditions today. Many scientists now suspect that those two groups diverged from a common ancestor relatively soon after life began. Millions of years after the development of archaea and bacteria, the ancestors of today’s eukaryotes split off from the archaea (Figure 4.1).

Figure 4.1 The three main branches of the phylogenetic tree of life.”

ProkaryoTeS—BacTeria and archaea

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Domain Bacteria

Bacteria are primitive microscopic single-celled organisms (Figure 4.2) that exist in mind-numbing numbers. Estimates suggest there may be approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants and animals. There is no consen-sus on how many species of bacteria may be out there (or in there). Numbers of bacterial species are thought to range somewhere between 120,000 to 150,000, but many microbiologists believe those numbers may be just the tip of the iceberg.

Bacteria are found everywhere above, on, and in this planet. Soil may contain 40 million of them per gram, and fresh water 1 million per milliliter. Bacterial cells may be collected at 10,058m (33,000 feet) in the air and in ocean sediments on the bottom of the Mariana Trench 11 kilometers (7 miles) down. In fact, researchers have found bacteria thriving inside the rocks that make up the sea floor. Bacteria are also found in large numbers on and in other living creatures, including humans, as Neil DeGrasse Tyson’s opening quote and the Introduction section reveal.

Bacteria RevealedThe hidden realm of prokaryotes was first revealed to humans with the invention of the microscope. One of the first microscopists was Englishman Robert Hooke (Figure 4.3). Hooke is known as a “Renaissance Man” of 17th century England for his work areas such as engineering, architect, astronomy, physics, and biology. Hooke’s most important publication was Micrographia, a 1665 volume document-ing observations he had made with a microscope (Figure 4.4). In this groundbreaking study, he coined the term “cell” while discussing the structure of cork; the boxlike cells of cork bark reminded him of the cells

(sleeping rooms) of a monastery. He also described flies, feathers, and snowflakes, and correctly identified fossils as remnants of once-living things.

Dutchman Antoni van Leeuwenhoek (Figure 4.5) was the first to observe and accurately describe microbial life. Although a drapery merchant by trade, Leeuwenhoek learned to grind lenses, made simple microscopes, and began observing with them. He seems to have been inspired to take up microscopy by having seen a copy of Hooke’s illus-trated book Micrographia, that depicted Hooke’s own observations with the microscope and was very popular.

Leeuwenhoek is known to have made over 500 “microscopes,” of which fewer than ten have survived to the present day. In basic design,

Figure 4.2 Colorized scanning electron micrograph of Escherichia

coli grown in culture.

Figure 4.3 Robert Hooke (1635-1703)

Figure 4.4 Hooke’s microscope was made by London instrument maker Christopher Cock. Light

from an oil lamp passing through a water flask illuminated


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probably all of Leeuwenhoek’s instruments—certainly all the ones

Figure 4.5 Antoni van Leeuwenhoek (1632-1723)

that are known—were simply powerful magnifying glasses, not com-pound microscopes of the type used by his contemporaries (Figure 4.6). However, because of various technical difficulties in building them, early compound microscopes were not practical for magnify-ing objects more than about twenty or thirty times natural size. Leeuwenhoek’s skill at grinding lenses, together with his naturally acute eyesight and great care in adjusting the lighting where he worked, enabled him to build microscopes that magnified over 200 times, with clearer and brighter images than any of his colleagues could achieve. What further distinguished him was his curiosity to observe almost anything that could be placed under his lenses and his care in describing what he saw. Because he could not draw well, Leeuwenhoek hired an illustrator to prepare drawings of the things he saw, to accompany his written descriptions.

Leeuwenhoek turned his glass on anything he could get under his lens—pond water in which he saw protists for the first time, sperm, blood, and even the plaque from his own teeth in which he saw bacteria for the first time. Leeuwenhoek was not a trained scientist and as such had lit-tle standing in the scientific community. However, through his communications with the Royal Society of London and their publication of his letters and illustrations, Leeuwenhoek gained great notoriety and eventually membership into the Royal Society.

Technological advances over the crude light microscopes of Hooke and Leeuwenhoek have led to the development of fluorescence light microscopes that allow us to see fluores-cent-labeled cellular structures in great detail and scanning electron microscopes that use electrons instead of light waves allowing scientists to magnify a specimen up to 10,000,000 times its original size.

Nature of LifeThe history of microbiology entwines the stands of visualizing the unseen (microscopy) and the investiga-tion of the nature of infectious diseases. This history is also entwined with the prolonged debate about how living things arise. Leeuwenhoek and other of his time and those that came after him believed that the little “animalcules” he observed sprang forth from inanimate matter, a belief known as spontaneous generation. Rotten meat was thought to generate fly maggots, rags were thought to generate rats and mice, and leaves falling into a pond were thought to generate fish were, but some of the many incorrect inferences about the origin of individual organisms made at that time.

Figure 4.6 The specimen was mounted on the sharp point that sticks up in front of the lens, and its position and focus could be adjusted by turning the two screws. The entire instrument was only 3-4 inches long, and had to be held up close to the eye; it required good lighting and great patience to use.


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One of the first scientists to experimentally challenge the notion of

Figure 4.7 Francesco Redi (1626-1697)”

spontaneous generation was Francesco Redi, an Italian physician, naturalist, biologist, and poet (Figure 4.7). Redi took six jars and divided them into two groups of three: In one experiment, in the first jar of each group, he put an unknown object; in the second, a dead fish; in the last, a raw chunk of veal. Redi covered the tops of the first group of jars with fine gauze so that only air could get into it. He left the other group open. After several days, he saw maggots appear on the objects in the open jars, on which flies had been able to land, but not in the gauze-covered jars. In the second experiment, meat was kept in three jars. One of the jars was uncovered, and two of the jars were covered, one with cork and the other one with gauze. Flies could only enter the uncovered jar, and in this, maggots appeared. In the jar that was covered with gauze, maggots appeared on the gauze but did not survive (Figure 4.8).

Figure 4.8 A generalized representation of Redi’s experiments disproving abiogenesis of flies.”

He continued his experiments by capturing the maggots and waiting for them to metamorphose, which they did, becoming flies. Also, when dead flies or maggots were put in sealed jars with dead animals or veal, no maggots appeared, but when the same thing was done with living flies, maggots did appear. We will visit Redi’s experiments in his own words later in Box 20.1.

Although Redi and others after him thoroughly disproved the notion of abiogenesis, the advent of the microscope revived the controversy. As we began to see and better understand microbes, the abiogenesists reasoned that while it was true that large complex creatures like flies, frogs, and rats do not spontaneously generate, primitive single-celled creatures cer-tainly must do so. The final nail in the coffin of abiogenesis was driven in by the Frenchman Louis Pasteur (Figure 4.9) around 1859 in a series of Figure 4.9 Louis Pasteur

(1822-1895)


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classic experiments that showed that without contamination, microbes would not and could not appear. He demonstrated that in sterilized and sealed flasks no microbes ever appeared, but in sterilized flasks that were broken open and exposed to air, microorganisms would appear (Figure 4.10). Abiogenesis as a viable and logical theory to explain the origin of living things had been put to rest once and for all.

Figure 4.10 A generalized representation of Pasteur’s experiments disproving abiogenesis of microbes.

Microbes and Medicine

Understanding microbes led to a realization of the connection between disease and bacteria, an idea that came to be known as the germ theory of disease. That knowledge led microbiologists such as German physician Robert Koch (Figure 4.11) to identify the specific causative agents of tuberculosis, cholera, and anthrax, giving experimental support for the concept of infectious disease. Koch proposed four postulates to prove a causal relationship between a microorganism and a disease:

1. The organism must always be present, in every case of the disease.

2. The organism must be isolated from a host containing the dis-ease and grown in pure culture.

3. Samples of the organism taken from pure culture must cause the same disease when inoculated into a healthy, susceptible ani-mal in the laboratory.

4. The organism must be isolated from the inoculated animal and must be identified as the same original organism first isolated from the originally diseased host.

5. Better understanding of the link between microbes and disease would lead to efforts to prevent diseases through vaccinations and cure diseases through the discovery and medical application of antibiotics.

Figure 4.11 Robert Koch (1843-1910)


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Characteristics of Bacteria

Because of their small size (microscopic) and primitive nature, bacteria display few morphological and ana-tomical characteristics.

Figure 4.12 The average diameter of spherical bacteria (cocci) is 0.5-2.0 µm. For rod-shaped (bacilli) or filamentous bacteria, average length is 1-10 µm and average diameter is 0.25-1 .0 µm.

Bacterial Structure All bacterial cells are microscopic, but that certainly does not tell the whole story (Figure 4.12).

• Typical plant and animal cells are around 10 to 50 µm in diameter with plant cells averaging 10-100 µm long whereas animal cells average 10-30 µm long.

• Escherichia coli, an average size bacillus, is 1.1 to 1.5 µm wide by 2.0 to 6.0 µm long.• One group of bacteria called the Mycoplasmas, measure about 0.25 µ and are the smallest cells

known so far. Mycoplasma gallicepticum, with a size of approximately 200 to 300 nm are thought to be the world smallest bacteria.

• At 200–750 μm in diameter, Thiomargarita namibiensis, a gram-negative Proteobacterium found in the ocean sediments off the coast of Namibia, is the world’s largest bacteria and can be seen with the unaided eye.


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Figure 4.13

The most obvious morphological characteristic of bacteria is their shape. Although there may be mil-lions of species of bacteria, nearly all of them exhibit one of five basic shapes: (Figure 4.13)

• Cocci are spherical.• Bacilli are rod-like.• Spirilli are helical with rigid bodies.• Vibrios look like curved rods.• Spirochetes are helical with flexible bodies.

Pleomorphic bacteria can alter their shape and size in response to environmental conditions, and a few types are even star-shaped or square. Cell shape is characteristic of a given bacterial species but can vary depending on growth conditions. Some bacteria have complex life cycles involving the production of stalks and appendages, and some produce elaborate structures bearing reproductive spores.

Bacteria are bounded by a cell wall composed of the unique molecule peptidoglycan, a complex of polysaccharides linked by amino acids. Bacteria may be categorized into two types based on the structure of their cell wall—Gram-positive bacteria and Gram-negative bacteria.


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Figure 4.14

Gram-positive bacteria have a very thick peptidoglycan cell wall relative to the thin-walled Gram-negative bacteria. Furthermore, Gram-negative bacteria are surrounded by a second plasma membrane outside the cell wall that blocks antibiotic drugs, making Gram-negative infections more difficult to treat. The two types may be distinguished from each other by the use of Gram staining techniques. After application of the stain, Gram-positive bacteria appear dark purple whereas Gram-negative bacteria appear red, providing a useful first step for identifying unknown bacteria causing an infection (Figure 4.14).

Figure 4.15 Cell structure of a Gram-positive bacterium.”

Depending on the species, bacterial cells are variously equipped with flagella, fimbrae, pili, and a cap-sule (Figure 4.15). Bacteria flagella may occur singular or in tufts depending on the species and function


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to provide locomotion. Fimbrae and pili are long tubu-lar surface appendages that function for attachment, not locomotion. Fimbrae are longer and thicker than pili. The capsule(capsid) is a polysaccharide layer that is part of the outer envelope of a bacterial cell. It can be found in both Gram-positive and Gram-negative bacterial cells but should not be confused with the second lipid membrane found in Gram-negative bacteria. The capsule (capsid) helps protect the cell from engulfment by phagocytes. It also makes pathogenic bacteria more virulent because it shields the cells from antibiotics. Depending on the spe-cies some bacteria also form a slime layer (Figure 4.16).

The plasma membrane and cytoplasm of bacteria are essentially the same in structure and function as those of eukaryotic cells. Unlike eukaryotes, the bacte-rial DNA is not enclosed inside of a membrane-bound nucleus but instead floats free in the bacterial cytoplasm. This means that the transfer of cellular information through the processes of translation, transcription, and DNA replication all occur within the same compart-ment. Most bacterial DNA is circular although some examples of linear DNA exist. Along with chromo-somal DNA, most bacteria also contain small independent pieces of DNA called plasmids that often encode for traits that are advantageous but not essential to their bacterial host (Figure 4.17). Plasmids can be easily gained or lost by a bacterium and can be transferred between bacteria as a form of horizontal gene transfer.

Unlike eukaryotes, bacterial cells contain no mem-brane bound organelles. They do, however, possess ribo-somes, the site of protein synthesis in all living cells. It was once thought that prokaryotic cells did not possess cytoskeletons, but recent advances in visualization tech-nology and structure determination have shown that cytoskeletal filaments indeed exist in bacterial cells. In fact, homologs for all major cytoskeletal proteins in eukaryotes have been found in prokaryotes.

Bacterial MetabolismBacteria are very diverse in terms of obtaining the nutri-ents they need to survive. In most regards, bacteria are not much different than eukaryotic cells with respect to basic nutritional requirements. One major difference, however, concerns the need for oxygen. Most bacteria and all eukaryotic cells are aerobic. That is, they require

Figure 4.17 Plasmids replicate independently from the main chromosomal DNA and are not essential to the survival or replication of their host. Plasmids are

thought to be part of the bacterial domain’s mobilome, a sort of genetic commonwealth which most, if not all, bacterial cells can pull from, incorporate and

express. Plasmids can replicate inside a host and then move to another cell via horizontal genetic transfer.

Figure 4.16 Some bacterial cells produce a slime layer or capsid (capsule) of unorganized extracellular material that surrounds the cell. A biofilm develops when many

bacteria share a common slime layer. The difference between a capsid and a slime layer is somewhat arbitrary.

Capsids (capsules) are usually more tightly bound to the cell and not easily washed away as is a slime layer.


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a constant supply of oxygen to carry out cellular respiration. On the other hand, some bacteria are facultative anaerobes can grow in either the presence or absence of oxygen whereas still others are obligate anaerobes and are unable to grow in the presence of free oxygen.

Bacterial metabolism can be arranged into basic categories:• Autotrophic• Heterotrophic• Mixotrophic

Autotrophic bacteria can be categorized as photoautotrophs or chemoautotrophs. Photoautotrophs are pho-tosynthetic and use solar energy (light) as an energy source to synthesize organic compounds from carbon dioxide. Conversely, chemoautrotrophs utilize inorganic compounds such as hydrogen gas, hydrogen sul-fide, and ammonia as an energy source to synthesize organic compounds from carbon dioxide. The action of nitrifying bacteria in oxidizing ammonia (NH3) to nitrites (NO2 ¯) and nitrites to nitrates (NO3¯) keep essential nitrogen cycling ecosystems.

Chemoheterotrophic bacteria use organic compounds as both carbon and energy sources. Chemoheterotrophs live off nutrients they scavenge from living host as commensals or parasite or as saprophytes decaying dead organic matter of all kind. Chemoheterotrophic microbes are extremely abundant in nature and are respon-sible for the breakdown of large organic polymers such as cellulose, chitin, or lignin which are mostly indi-gestible to animals.

CyanobacteriaCyanobacteria are Gram-negative bacteria that are photosynthetic in nature and aquatic in habitat. Cyanobacteria get their name from the bluish-green pigment phycocyanin that they use to capture light for photosynthesis. However, not all blue-green bacteria are blue; some common forms are red or pink from the pigment phycoerythrin. These bacteria are often found growing on greenhouse glass, or around sinks and drains. The Red Sea gets its name from occasional blooms of a reddish species of Oscillatoria, and African flamingos get their pink color from eating Spirulina and tiny shrimp.

Figure 4.18 Cyanobacteria come in several forms. (a) Single-celled Prochlorococcus; (b) colonial Gleocapsa;(c) filamentous Anabaena with a clear heterocyst (left) and a akinete (right).

Heterocysts are sites of nitrogen fixation whereas akinetes are vegetative resting cells.


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Cyanobacteria are large cells and can be single-celled, colonial, or filamentous in form (Figure 4.18). They are common in both fresh and marine waters, in soil, and on moist surfaces. Cyanobacteria are sym-biotic with a number of organisms, including liverworts, ferns, and some invertebrates such as corals. In association with fungi, they form lichens that can grow on rocks and tree bark.

Bacterial ReproductionBacteria reproduce primarily by binary fission. In this process, the bacterium, which is a single cell, divides into two identical daughter cells. Binary fission begins when the DNA of the bacterium divides into two (replicates). The bacterial cell then elongates and splits into two daughter cells each with identical DNA to the parent cell. Each daughter cell is a clone of the parent cell (Figure 4.19).

Figure 4.19 Under the right conditions, binary fission can double the number of bacteria every 10 to 30 minutes,


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Although sexual reproduction does not occur in bacteria, three means of genetic recombination have been observed:

• Conjugation in which two bacteria temporarily link by means of a conjugation pilus or conjugation tube (Figure 4.20). While they are linked, the donor cell passes DNA to the recipient cell in the form of a plasmid.

• Transformation occurs when a cell picks up free float-ing pieces of DNA secreted by live bacteria or released by dead bacteria.

• Transduction occurs when bacteriophage viruses carry portions of DNA from one bacterial cell to another.

Domain Archaea

The scientific community was understandably shocked in the late 1970s by the discovery of an entirely new group of organisms—the Archaea. Dr. Carl Woese and his colleagues at the University of Illinois were studying relationships among the prokaryotes using DNA sequences and found that there were two dis-tinctly different groups. Those “bacteria” that lived at high temperatures or produced methane clustered together as a group well away from the usual bacteria and the eukaryotes. Because of this vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota, Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was a misnomer, and shortened it to Archaea.

Archaea have characteristics that distinguish them from both bacteria and eukaryotes:• The plasma membrane of archaea contains unusual

lipids that allow many of them to function at high temperatures. The lipids of archaea contain glycol linked to branched-chain hydrocarbons, in con-trast to the lipids of bacteria that contain glycol linked to fatty acids.

• The cell walls of archaea do not contain pepti-doglycan as do the cell walls of bacteria. In some archaea, the cell wall is largely composed of poly-saccharides, and in others, the cell wall is pure pro-tein. A few have no cell wall.

Archaeans are often referred to as extremophiles because they inhabit some of the most extreme environments on the planet. Some, known as thermophiles, live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs, or in extremely alkaline or acid waters (Figure 4.21). Methanogens have been found thriving inside the digestive tracts of cows, termites, and marine life

Figure 4.20

Figure 4.21 An aerial view of Grand Prismatic Spring, Yellowstone National Park. Thermophilic

archaea are responsible for the bright rings of color that surround the spring. Coating

the rock in large bacterial mats, their energy-harnessing pigments dictate the colors that surround the water. If the bacteria contain

more chlorophyll, the mats will be more green in color and if they contain more carotenoids,

the bacterial carpet will be more yellowish, reddish or orangish depending on the species.”


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where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum deposits deep underground, and halophytes can survive the desiccating effects of extremely saline waters.

Although archaea are capable of surviving in environmentally extreme conditions, they are found in more moderate conditions as well. Archaeans are quite abundant as part of the phytoplankton of the open ocean, and some live in symbiotic relationships with animals, such sponges, and sea cucumbers. There are no parasitic archaeans—that is, they are not known to cause infectious diseases.

In Summary

• Biologists recognize three main branches on the tree of life. These branches, known as domains, are Archaea, Bacteria, and Eukaryota.

• Archaea and Bacteria are prokaryotes because their cells have nuclei not contained within a mem-brane and they lack organelles. Eukaryota are designated as eukaryotes because their cells have a membrane-bound nucleus and numerous complex organelles.

• Archaea and bacteria first appeared around 3.5 billion years ago and later eukaryotes split off from the archaea.

• Bacteria are primitive microscopic single-celled organisms that exist in mind-numbing numbers.• Bacteria are found everywhere above, on, and in this planet.• Bacteria became known through the work of early microscopists Hooke, Leeuwenhoek, and others.• Spontaneous generation or Aristotelian abiogenesis is the belief that living things can sponta-

neously generate from dead organic or inorganic matter.• Francesco Redi disproved the spontaneous generation of flies in a classical experiment.• Louis Pasteur disproved the spontaneous generation of microbes with his gooseneck flask

experiment.• Bacteria come in different sizes, both in length and diameter.• Bacteria come in five basic shapes:

○ Coccus- spherical. ○ Bacillus-rod-like. ○ Spirillum-helical with rigid bodies. ○ Vibrios-curved rods. ○ Spirochetes-helical with flexible bodies.

• Pleomorphic bacteria can alter their shape and size in response to environmental conditions, and a few types are even star-shaped or square.

• Bacteria may be categorized into two types based on the structure of their cell wall—Gram-positive bacteria and Gram-negative bacteria.

• Depending on the species, bacterial cells are variously equipped with flagella, fimbrae, pili, and a capsule.

• Bacterial DNA is not enclosed inside of a membrane-bound nucleus but instead floats free in the bacterial cytoplasm.


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• Most bacteria also contain small independent pieces of DNA called plasmids that often encode for traits that are advantageous but not essential to their bacterial host.

• Bacteria possess ribosomes and cytoskeletal fibers.• Most bacteria are aerobic and require free oxygen, but some others are anaerobes that cannot sur-

vive in the presence of free oxygen/• Bacterial metabolism can be arranged into basic categories:

○ Autotrophic ○ Heterotrophic ○ Mixotrophic

• Cyanobacteria are Gram-negative bacteria that are photosynthetic in nature and aquatic in habi-tat. They are common in both fresh and marine waters, in soil, and on moist surfaces.

• Cyanobacteria are large cells that can be single-celled, colonial, or filamentous in form.• Bacteria reproduce by binary fission.• Although sexual reproduction does not occur in bacteria, three means of genetic recombination

have been observed: ○ Conjugation ○ Transformation ○ Transduction

• Archaea are bacteria-like protists that are placed in their own domain.• Archaeans are often referred to as extremophiles because they inhabit some of the most extreme

environments on the planet.

Review and Reflect

1. Pick a Side You have been given two cultures—a culture of prokaryote cells and a culture of eukaryote cells. How would you determine which culture was which type of cell? Imagine you have access to all the scientific equipment you need, including an electron microscope.

2. They’re Everywhere Man Speaking biologically and ecologically, are bacteria really everywhere? Explain

3. Are You Positive? Again you have been given two cultures—a culture of Gram-positive bacteria and a culture of Gram-negative bacteria. Explain what process you would go through to identify which culture was which.

4. Eezy Peezy Which type of bacteria—autotrophic or chemoheterotrophic—would be the easiest to maintain long-term in a laboratory? Explain

5. Sicky Chicky Throughout France In the mid-1800’s chickens were dying of chicken cholera. Scientists were able to identify a particular bacterium as the cause of the disease. Each time a cul-ture of young bacteria was injected into healthy chickens, they developed cholera and died.

One day, a researcher injected some bacteria that were several weeks old but still alive into healthy chickens. As usual, the chickens developed symptoms of cholera. By the next day, how-ever, all the chickens had recovered.A. List as many possible explanations as you can for why the chickens did not die.


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Suppose the scientists conducted the following experiment: A large group of chickens was divided into two similar groups. Group A was injected with young bacteria while Group B was injected with the same amount of old bacteria. Both groups were kept under identical conditions. Chickens in both groups develop symptoms of cholera. By the next day, all of the chickens in Group A were dead while all of those in Group B had recovered.

B. Form a hypothesis to explain this outcome.C. Can you think of how the scientists put this information to practical use?

6. Bacteria Run Amok Bacteria can asexually reproduce through binary fission at rates that truly boggle the mind. Starting with 1 bacterium and assuming a reproductive rate of one division every 20 minutes, how many bacteria would there be at the end of 40 minutes? 1 hour? 12 hours? (Also assume unlimited food and space and that no bacteria die).

7. Good Teeth, Bad Teeth Streptococcus mutans obtains energy by oxidizing sucrose. This bacterium is abundant in the mouth of Western European and North American children where it is a promi-nent cause of cavities. This bacterium is virtually absent in children from East Africa, where tooth decay is rare. Propose a hypothesis to explain this discrepancy. Outline the design of a study that would test your hypothesis.

8. Prune the Tree Examine Figure 20.1 that depicts the phylogenetic tree for the three domains. It proposes that Bacteria and Archaea arose from the same common ancestor and later eukaryotes developed from the archaea lineage. Other hypotheses place the Archaea as the ancestors to all other organisms. Sketch a phylogenetic tree that presents Bacteria and Eukaryota as more closely related to each other than to Archaea, and has Archaea as a sister group to Bacteria and Eukaryota.

9. Does the Relationship Work? The nitrogen-fixing bacterium Rhizobium “infects” the roots of some plant species where it is believed that the bacterium provides nitrogen, and the plant pro-vides carbohydrates from photosynthesis. The table below is data gathered by scientists when they measured the 12-week growth of the plant Acacia irrorata (green wattle) when infected with six different Rhizobium species. Graph the data and then interpret the graph. Did Rhizobium benefit the plant and which strain was the most beneficial?

Rhizobium strain 1 2 3 4 5 6

Plant mass (g) 0.91 0.06 1.56 1.72 0.14 1.03

Note: Without Rhizobium, after 12 weeks, Acacia plants have a mass of about 0.1 g.Source: J. J. Burdon, et al. Variations in the effectiveness of symbiotic associations between native rhizobia and temperate Australian Acacia: within species interactions. Journal of Applied Ecology 36:398-408 (1999).

10. Take Your Pills People taking antibiotics for a bacterial illness often feel better after a short while so they stop taking the antibiotic. Explain how this might result in the evolution of drug-resistant bacteria.


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11. Table of Suffering For countless centuries bacterial diseases have wrought suffering and death to humankind. Prepare a table in which you detail: (1) the main bacterial diseases that infect humans, (2) the causative bacterium for each disease, and (3) the symptoms and effects of the disease on the individual.

Create and Connect

1. Does Life Arise Spontaneously?—A Classic Experiment One of the great precepts or scientific laws of modern biology is that “life begets life.” We accept without question that every living thing, regardless of size and complexity, attains life from the asexual or sexual reproduction of oth-ers of its kind and that life flows across the generations in an uninterrupted stream. However, for millennia, humankind believed just the opposite. Life was thought to spring from slime, putrefac-tion, or a host of other unlikely inorganic origins. This corruption of the truth was based solely on flawed observations and conjectures and began to unravel with the application of experimentation to the question. In 1688, the Italian, Francesco Redi, fired one of the first salvos in the war on the theory of spontaneous generation. Despite the clarity of Redi’s results, the spontaneous generation theory survived. Its adherents were obliged to shift the battleground to the realm of microbiology where the decisive final battles were fought by Pasteur and Tyndall in the nineteenth century. Read, analyze, and above all, appreciate this classic experiment. Answer the questions that follow.

Box 4.1 Experiments on the Generation of Insects by Francesco Redi (Translated from the 1688 edition by Mab Bigelow)

“Although content to be corrected by anyone wiser than myself, if I should make any erroneous statements, I shall express my belief that Earth, after having brought forth the first plants and animals at the beginning by order of the Supreme and Omnipotent Creator, has never since produced any kinds of plants or animals, either perfect or imperfect; and everything which we know in past or present times that she has produced, came solely from the true seeds of the plants and animals themselves, which thus, through means of their own, preserve their species. And, although it be a matter of daily observation that infinite numbers of worms are produced in dead bodies and decayed plants, I feel, I say, inclined to believe that those worms are all generated by insemination and that the putrefied matter in which they are found has no other office than that of serving as a place, or suitable nest where animals deposit their eggs at the breeding season, and in which they also find nourishment; or otherwise, I assert that nothing is ever generated therein…

At the beginning of June I ordered to be killed three snakes, the kind called eels of Aesculapius. As soon as they were dead, I placed them in an open box to decay. Not long afterward I saw that they were covered with worms of a conical shape and apparently without legs. These worms were intent on devouring the meat, increas-ing meanwhile in size, and from day to day I observed that they likewise increased in number; but, although of the same shape, they differed in size, having been born on different days. But all, little and big, after having


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consumed the meat, leaving only the bones intact, escaped from a small aperture in the closed box, and I was unable to discover their hiding place. Being curious, therefore, to know their fate, I again prepared three of the same snakes, which in three days were covered with small worms. These increased daily in number and size, remaining alike in form, though not in color. Of these, the largest were white outside, and the small ones, pink. When the meat was all consumed, the worms eagerly sought an exit, but I had closed every aperture. On the nineteenth day of the same month, some of the worms ceased all movements, as if they were asleep, and appeared to shrink and gradually assume a shape like an egg. On the twentieth day all the worms had assumed the egg shape, and had taken on a golden white color, turning to red, which in some darkened, becoming almost black. At this point the red, as well as the black ones, changed from soft to hard, resembling somewhat those chrysalides formed by caterpillars, silkworms, and other insects. My curiosity being thus aroused, I noticed that there was some difference in shape between the red and black eggs [pupae],1 though it was clear that all were formed alike of many rings joined together; nevertheless, these rings were more sharply outlined, and more apparent in the black than in the red, which last were almost smooth and without slight depression at one end, like that in a lemon picked from its stalk, which further distinguished the black egg-like balls.

I placed these balls separately in glass vessels, well covered with paper, and at the end of eight days, every shell of the red balls was broken and from came forth a fly of gray color, torpid and dull, misshapen as if half finished, with closed wings; but after a few minutes they commenced to unfold and expand in exact proportion to the tiny body, which also in the meantime had acquired symmetry in its parts. Then the whole creature, as if made anew, having lost its gray color, took on a most brilliant and vivid green; and the whole body had expanded and grown so that it seemed incredible that it could ever have been contained in the small shell. Though the red eggs [pupae] brought forth green flies at the end of eight days, the black ones labored fourteen days to produce certain large black flies striped with white, having a hairy abdomen, of the kind that we see daily buzzing about butchers’ stalls.…

I continued similar experiments with the raw and cooked flesh of the ox, the deer, the buffalo, the lion, the tiger, the dog, the lamb, the kid, the rabbit; and sometimes with the flesh of ducks, geese, hens, swallows, etc., and finally I experimented with different kinds of fish, such as swordfish, tuna, eel, sole, etc. In every case, one or other of the abovementioned kinds of flies were hatched, and sometimes all were found in a single animal. Besides these, there were to be seen many broods of small black flies, some of which were so minute as to be scarcely visible, and almost always I saw that the decaying flesh and the fissures in the boxes where it lay were covered with not alone with worms, but with the eggs from which, as I have said, the worms were hatched. These eggs made me think of those deposits dropped by flies on meats, that eventually become worms, a fact noted by the compilers of the dictionary of the Academy, and also well known to hunters and to butchers, who protect their meats in Summer from filth by covering them with white cloths. Hence great Homer in the nineteenth book of the Iliad, has good reason to say that Achilles feared lest the flies would breed worms in the wounds of dead Patroclus, whilst he was preparing to take vengeance on Hector.

A. Would you say Redi was a thorough experimenter? Explain.B. What did Redi mean when he said, “Belief would be vain without the confirmation of the

experiment.”


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C. Describe at least one of the several experiments that Redi discusses in this work. Your descrip-tion should include the Methods and Materials Redi used and the Results he obtained from the experiment.

D. After conducting a number of experiments on many kinds of flesh, what was Redi’s general conclusion about the origin of flies in relation to the decaying meat?

2. Food Poisoning—A Case Study Every year, thousands of cases of bacterial food poisoning are reported. In each case, a medical detective is assigned to find out how the person got food poison-ing. Once the cause of the food poisoning has been determined, the medical detective can move to correct the conditions that led to the food poisoning.

Two types of bacteria that cause food poisoning are salmonella and staphylococci. A medical detective knows that these bacteria produce very different symptoms. So in order to determine which bacteria is the culprit, the detective will ask a series of important questions. The first thing the detective will want to know is exactly what the patient ate in the 24 hours prior to becoming ill and where the food was eaten. Other important information that the detective will gather includes how long after eating the patient became ill and whether the patient developed a fever. The detective will also want to know if the patient developed chills. Armed with answers to these questions, the detective can determine what caused the food poisoning and which meal contained the tainted food but how?

The medical detective knows many details about these two types of bacterial food poisoning. For example, staphylococci produce a toxin, or poison, that is secreted into the food source as the bacteria multiply. Once a person eats the tainted food, the toxin will be carried throughout his or her body by the bloodstream. Within a few hours after the food has been ingested, the toxin will usually cause symptoms that include diarrhea, vomiting, nausea, and abdominal cramps. Fortunately, recovery is usually complete 24 to 48 hours after the onset of the symptoms.

Like staphylococci, salmonella produce a toxin. This toxin, however, is contained in the bacteria’s cell walls and is released only when the bacteria lyse, or burst. Because of this difference, the symptoms produced by salmonella are somewhat unlike those produced by staphylococci. For example, it takes longer for a person to feel the effects of salmonella, often 12 hours or more. Salmonella infections almost always cause diarrhea. And they also generally result in a fever, chills, frequent vomiting, and abdominal pain. It may also take a patient quite a bit longer to recover from a case of salmonella food poisoning.

Now it is time for you to become a medical detective.

Case Study 1: A patient with food poisoning reports that he ate his last meal at about 6 P.M. Although he felt fine the next morning, the patient became very sick at work. Due to severe abdominal pain and vomiting, the patient returned home. The patient also had a fever, chills, and severe diarrhea. He still felt sick the next day and did not fully recover for several days.

Case Study 2: You interview a patient who is suffering from food poisoning. However, this patient shows signs of recovery and feels well enough to go back to work. You discover that the last time the patient ate was about 6 P.M. the night before. While watching television later that evening,


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the patient became ill and had extremely severe abdominal cramps. The patient had a mild case of diarrhea that has subsided. There was no fever.

Analyze each case study to determine whether the food poisoning was caused by salmonella or staphylococci. Support your diagnoses based on the data provided.

3. Friend or Foe? Life on this planet would not be possible, yet bacterial pathogens have wiped out countless millions of humans during our history as a species. You are the science editor of a large metropolitan newspaper. Your editor has given you the following assignment: Write a newspaper column in which you detail the importance of bacteria, both positive and negative. How would you proceed and what would you say? Format your work as if it were an actual newspaper article.

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