Microbiology - Advanced

Douglas Wilkin, Ph.D. Niamh Gray-Wilson

Say Thanks to the Authors Click http://www.ck12.org/saythanks (No sign in required) AUTHORS Douglas Wilkin, Ph.D. To access a customizable version of this book, as well as other Niamh Gray-Wilson interactive content, visit www.ck12.org EDITOR Douglas Wilkin, Ph.D.

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Printed: January 24, 2016 www.ck12.org Chapter 1. Microbiology - Advanced

CHAPTER 1 Microbiology - Advanced

CHAPTER OUTLINE 1.1 Prokaryotes - Advanced 1.2 Prokaryote Classification - Advanced 1.3 Prokaryote Structure and Function - Advanced 1.4 Gram Stain Identification - Advanced 1.5 Prokaryote Intracellular Structures - Advanced 1.6 Prokaryote Extracellular Structures - Advanced 1.7 Introduction to Archaea - Advanced 1.8 Introduction to Bacteria - Advanced 1.9 Prokaryote Nutrition and Metabolism - Advanced 1.10 Prokaryote Habitats - Advanced 1.11 Prokaryote Growth and Reproduction - Advanced 1.12 Symbiotic Relationships of Prokaryotes - Advanced 1.13 Human Uses of Prokaryotes - Advanced 1.14 Prokaryotes and Research - Advanced 1.15 Bacterial Diseases - Advanced 1.16 Prokaryotic Infections - Advanced 1.17 Preventions and Treatments for Bacterial Diseases - Advanced 1.18 Emerging and Reemerging Diseases - Advanced 1.19 Control of Bacteria - Advanced 1.20 Microbiology of Viruses - Advanced 1.21 Virus Characteristics - Advanced 1.22 Virus Structure - Advanced 1.23 Virus Discovery - Advanced 1.24 Virus Classification - Advanced 1.25 Virus Origins - Advanced 1.26 Virus Replication - Advanced 1.27 Lytic Cycle - Advanced 1.28 Lysogenic Cycle - Advanced 1.29 Viral Disease - Advanced 1.30 Control of Viruses - Advanced 1.31 Viruses in Research - Advanced 1.32 Prions and Viroids - Advanced 1.33 References

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Introduction

Can you guess what type of organism is pictured here? Are they fat green worms on a red leaf? Here’s a clue: there are more organisms like these than any other on Earth. Here’s another clue: each organism consists of a single cell without a nucleus. And lastly, there are more of these types of organisms in your mouth than people on the planet. The specific organism depicted here are bacteria called Salmonella. If the word Salmonella rings a bell, that’s probably because Salmonella causes human diseases such as food poisoning. Many other types of bacteria also cause human diseases. But not all bacteria are harmful to people. In fact, we could not survive without many of the trillions of bacteria that live in or on the human body. You will learn why when you read this chapter.

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1.1 Prokaryotes - Advanced

• Define and describe prokaryotic organisms.

If you had to guess what these cells represent, what would you say? Single-celled organisms with a few flagella. If your first guess was some sort of prokaryotic organism, that would be correct. And if you could see inside, what would be missing?

Prokaryotes

Have you ever eaten cheese, yogurt, or pickled vegetables or had to take antibiotics? Have you ever had acne or a sore throat? If so, you have both benefited and suffered from the existence of prokaryotes. They are tiny and are sometimes bothersome, but the world would be a very different place without them. Prokaryotes are single-celled organisms without a nucleus. It is the lack of a nucleus that is the major distinction between prokaryotic cells and eukaryotic cells. Prokaryotic cells also lack other membrane-bound organelles, but they do contain ribosomes. Recall that ribosomes are not surrounded by a membrane. Prokaryotes are the most numerous organisms on Earth. Most are too small to be seen with the naked eye. Because of their tiny size, the existence of prokaryotes was unknown until Anton van Leeuwenhoek first saw tiny cells with his microscope in the late 17th century. Since then, prokaryotes have been found almost everywhere on Earth. They are found in sea water, in animals’ intestines, on your skin, and even in rocks deep beneath the Earth’s crust. Scientists estimate that life on Earth developed between 3 and 4 billion years ago and that the first types of cells were prokaryotes, possibly similar to those that live in an environment comparable to that shown in the Figure 1.1.

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Prokaryotes can survive on this planet just fine without us, but conversely, we could not survive without prokaryotes. Modern day bacteria and archaea comprise the two prokaryotic kingdoms.

FIGURE 1.1 The landscape of early Earth was hot and acidic and may have looked a little like Mammoth Hot Springs in Yellowstone National Park. Scientists believe that prokaryotic organisms, possibly similar to the ones living in the hot springs today, were the first organisms on Earth.

Vocabulary

• eukaryotic cells: Cells typical of multi-celled organisms; they have a nucleus and membrane bound organelles and are usually larger than prokaryotic cells.

• organelle: A structure within the cytoplasm of a cell that performs a specific function. They may be enclosed within a membrane.

• prokaryote: An organism that has neither a cell nucleus nor any organelles that are surrounded by a mem- brane; bacteria are prokaryotes.

• prokaryotic cells: Cells typical of simple single-celled organisms, such as bacteria; they lack a nucleus and other membrane bound organelles.

Summary

• Prokaryotes are single-celled organisms without a nucleus.

Practice

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/HippoCampus/Biology?loadLeftClass=Course&loadLeftId=37&loadTopicId=39 66

1. What is the major distinct characteristic of a prokaryote?

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2. Where are prokaryotes found? List some example environments. 3. How does other life benefit from prokaryotes? What process do prokaryotes carry out that is beneficial to other life? 4. How did ancient prokaryotes change the early Earth’s atmosphere?

Practice Answers

1. A prokaryote does not have a nucleus nor membrane bound organelles. 2. Bacteria are found in a very diverse range of environments. Archaea are found in extreme environments, including locations with excessive heat, cold, salinity, pH and pressure. Archaea are often found in more temperate environments as well. 3. Prokaryotes benefit other life through carrying out photosynthetic processes. They also play a significant role in nitrogen, sulfur, and carbon cycles. 4. Cyanobacteria are believed to have developed photosynthetic processes which increased the levels of oxygen in early Earth’s atmosphere.

Review

1. What are prokaryotic organisms? 2. What is the distinguishing feature between prokaryotic cells and all other cells? 3. Name some important beneficial human uses of prokaryotes.

Review Answers

1. Prokaryotes are single-celled organisms which do not have a nucleus. 2. Prokaryotic cells are distinguished from other cells through their lack of both a nucleus and membrane-bound organelles. 3. Prokaryotic organisms are necessary for the production of various foods, as well as the production of antibi- otics.

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1.2 Prokaryote Classification - Advanced

• Outline the relationship between bacteria, archaea, and eukaryotes.

What do all these organisms have in common? They are all bacteria. But more than that, they are all common bacteria that infect humans. Notice that they have different shapes and sizes.

Classification and Evolution of Prokaryotes

Even though prokaryotes are tiny organisms, they differ greatly in where they live, what they use for food, and their DNA sequences. In the past, scientists classified prokaryotes into two groups, called Eubacteria and Archaebac- teria. The kingdom Eubacteria was made up of the “everyday” bacteria, such as the ones that make milk sour, decompose dead organic matter, and, on occasion, make people sick. The kingdom Archaebacteria was made up of a strange group of microorganism that scientists found in extremely hot, acidic, or salty environments. In the late 1970s two American scientists, Carl Woese and George Fox, proposed that archaebacteria were not just "weird" bacteria, but instead were a distinct group of organisms that are very different from bacteria. Their idea was based on their investigations of certain prokaryotic DNA and RNA sequences.

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Genome Changes Over Time

The DNA sequence in the genome of organisms changes slowly over time. Certain sequences of DNA change more slowly than other sequences do. These stable sequences usually contain genes that code for molecules involved in important processes, such as protein synthesis. For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly. Therefore, comparison of the DNA sequences within these genes is useful for investigating the evolutionary relationship between groups of organisms that evolved from a common ancestor millions or billions of years ago. This type of analysis is known as molecular phylogenetic analysis. The small-subunit ribosomal RNA (SSU rRNA) gene is the gene used most widely for this analysis. All cells have ribosomes, so all cells have rRNA genes.

Three Domain Classifications

The three-domain system is a biological classification system introduced by Carl Woese and his colleagues in 1990. The classification system divides all organisms into three large groups, or domains. These are Domain Archaea, Domain Bacteria, and Domain Eukarya. Domains Bacteria and Archaea are made up of prokaryotic cells. Domain Eukarya is made up of eukaryotic cells. The understanding is that archaea, bacteria, and eukaryotes each arose from a common ancestor. The Figure 1.2 shows a proposed relationship between the three domains that is based on the analysis of a rRNA gene (See the Classification concepts for additional information). Surprisingly, archaea are more closely related to eukaryotes than bacteria are. They have many genes that are more similar to eukaryotes than bacteria. However, debate remains as to what prokaryotic cell type came first; did archaea evolved from bacteria, or did archaea and bacteria both split off from a common ancestor at about the same time? To learn more about phylogenetic classification, see the Classification concepts.

FIGURE 1.2 A phylogenetic diagram based on riboso- mal RNA gene analysis. Domain Bacteria and Archaea are made up of prokaryotic cells. Domain Eukarya is made up of eukaryotes. The exact relationships be- tween the three domains are still being debated.

Vocabulary

• Archaebacteria: Unicellular microorganisms in the domain Archaea; they are genetically distinct from both bacteria and eukaryotes. They often inhabit extreme environments.

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• Eubacteria: True bacteria; eubacteria includes all bacteria except for archaebacteria.

• three-domain system: The classification system that divides all organisms into three large groups, or do- mains: Domain Archaea, Domain Bacteria, and Domain Eukarya.

Summary

• Domain Bacteria and Domain Archaea are made up of prokaryotic cells. Domain Eukarya is made up of eukaryotes. • The exact relationships between the three domains are still being debated. • Archaea have many genes that are similar to eukaryotic genes, but they also have genes that are similar to bacterial genes.

Practice

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/HippoCampus/Biology?loadLeftClass=Course&loadLeftId=37&loadTopicId=39 66

1. What are the two distinct clades of prokaryotes? 2. How do eubacteria and archaebacteria differ at the molecular level? 3. How are archaebacteria more closely related to eukaryotes than eubacteria? 4. What types of extreme environments can archaebacteria be found in? 5. Why may archaebacteria be more widespread than previously thought?

Practice Answers

1. Bacteria and Archaea are the two distinct clades of prokaryotes. 2. Eubacteria and archaebacteria have distinct differences in their DNA and RNA. 3. Archaea are prokaryotes but have chemical and structural features in common with eukaryotes. 4. Some archaea live in conditions of excessive heat, cold, salinity, pH, and pressure. 5. Many archaea inhabit temperate habitats, making them more widespread than previously thought.

Review

1. Outline the origin of the three domain system of classification. 2. Distinguish between archaebacteria and eubacteria.

Review Answers

1. The three-domain system is a biological classification system introduced by Carl Woese and his colleagues in 1990. The classification system divides all organisms into three large groups, or domains. These are Domain Archaea, Domain Bacteria, and Domain Eukarya. Domains Bacteria and Archaea are made up of prokaryotic cells. Domain Eukarya is made up of eukaryotic cells. The understanding is that archaea, bacteria, and eukaryotes each arose from a common ancestor. 2. The kingdom Eubacteria was made up of the “everyday” bacteria, such as the ones that make milk sour, decompose dead organic matter, and, on occasion, make people sick. The kingdom Archaebacteria was made up of a strange group of microorganism that scientists found in extremely hot, acidic, or salty environments.

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1.3 Prokaryote Structure and Function - Ad- vanced

• Identify structures unique to prokaryotic cells.

This is obviously a bacterial cell. What is the main clue? You could say it is the plasmids or the capsule. You could argue it is the flagellum or maybe even the cell wall around the single-celled organism. But the main clue is the lack of something. Where is the nucleus?

Structure and Function of Prokaryotes

Although prokaryotes are very small, they can be very different from each other. The shape of a prokaryotic cell can help it survive in its environment. They also have special structures within their cells and outside their cells that help them survive.

Cell Size

Most prokaryotes are much smaller than eukaryotic cells. Most prokaryotic cell diameters range from less than 1 µm to 5 µm, which means they can be seen only under a microscope. However, the largest known prokaryote, a bacterium called Thiomargarita namibiensis, has a diameter of up to 750 µm (0.75 mm), which is bigger than many eukaryotic cells. That is big enough to see with your own eyes.

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Cell Shape

Cell shape is one of the ways microbiologists identify and classify prokaryotes. A microbiologist is a biologist that studies prokaryotes and other microbes, such as protists and viruses. Prokaryotes come in many different shapes, but the most common shapes are spheres (cocci), rods (bacilli), and helices (spirilla), as shown in the Figure 1.3. Other prokaryote shapes include curved rods, long filaments, and even flat squares!

FIGURE 1.3 Prokaryotic Cell Shape. Three common shapes of bacterial cells. From left to right, spirilla, cocci, bacilli.

Though prokaryotes are generally classified as single-celled organisms, some species of prokaryotes can live in colonies of a few or even many cells. When grown in the laboratory on nutrient agar (a jelly-like substance that contains nutrients necessary for growth), a single prokaryote will multiply and form a colony that that can be easily seen with the naked eye, as shown in the Figure 1.4. Microbiologists can identify the microbe that made the colony by its shape, color, and the type of agar that it grows on.

FIGURE 1.4 A nutrient agar plate with colonies of Es- cherichia coli bacteria. Each colony was formed by a single cell (or colony forming unit) that multiplied over a given period of time.

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Plasma Membrane

The plasma membrane is a lipid bilayer that surrounds the cytoplasm of a prokaryotic cell. It physically separates the cytoplasm from the outside environment. The plasma membrane also works as a selectively permeable, or semipermeable, barrier that controls what enters and exits the cell. The plasma membrane contains certain types of lipids and proteins, but the type and number of lipids and proteins in the membrane depend on the species. The plasma membrane is discussed in Concept Cell Biology (Advanced). Proteins within the cell membrane receive and send signals that allow cells to communicate, or “talk,” with each other. Other proteins and molecules on the surface of the cell membrane serve as markers which identify cells. These markers help multicellular organisms’ immune cells recognize prokaryotic cells, often targeting the prokaryotic cell for destruction. The plasma membrane is also the site of many metabolic reactions for the prokaryotic organism, such as respiration, fermentation, and photosynthesis. Some prokaryotes, such as cyanobacteria, which carry out photosynthesis, have a plasma membrane with many little folds. This extra membrane surface area allows for greater metabolic activity.

Cell Wall

FIGURE 1.5 A Prokaryotic Cell. 1. Capsule 2. Cell wall 3. Plasma membrane 4. Cytoplasm 5. Ribosomes 6. Mesosome 7. Nucleoid (DNA) 8. Bacterial Flagellum.

Most prokaryotes have a cell wall which gives strength and rigidity to the cells, as well as the ability to withstand osmotic changes. The cell wall lies just outside the plasma membrane, as shown in the Figure 1.5. The structure of bacterial and archaeal cell walls differ. Bacteria and archaea can be identified by the structure of their cell walls, allowing identification of the prokaryote. Most bacterial cell walls contain peptidoglycans. Peptidoglycans are made up of a sugar and an amino acid molecule complex that form a mesh-like layer outside the cell membrane of bacteria. The amount of peptidoglycan in the cell wall differs between bacterial species. Archaea do not have peptidoglycan in their cell walls; instead, they have compounds such as glycoprotein (proteins with simple sugars attached), pseudopeptidoglycan, or polysaccharides. The nucleoid region of a prokaryotic cell is a region within the cytoplasm that contains the genetic material (DNA). As prokaryotic cells lack a nucleus, the genetic material is located in the cytoplasm. Many prokaryotic cells possess a single or few flagellum, which assist with movement. Mesosomes are folded invaginations in the cell membrane of bacteria, allowing for an increase in membrane surface area.

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Vocabulary

• cell wall: A rigid layer that surrounds the plasma membrane of prokaryotic cells and plant cells; it helps support and protect the cell.

• glycoprotein: A protein that contain oligosaccharide chains (glycans) covalently attached to polypeptide side- chains; they are often important integral membrane proteins, where they play a role in cell–cell interactions.

• microbiologist: A biologist that studies prokaryotes and other microbes, such as protists and viruses.

• peptidoglycan: A polymer found in the cell wall; they are made up of a sugar and amino acid molecule complex that form a mesh-like layer outside the plasma membrane of bacteria.

• plasma membrane: A thin coat of lipids (phospholipids) that surrounds and encloses a cell, forming a physical boundary between the intracellular space and the extracellular environment; it is also called the cell membrane.

Summary

• Bacteria have cells walls that contain peptidoglycan. Neither eukaryotes nor archaea contain peptidoglycan in their cell walls. • Both types of prokaryotes have cell walls, but many eukaryotic cells do not. • Neither type of prokaryotic cell has a nucleus or membrane-bound organelles.

Practice

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/HippoCampus/Biology?loadLeftClass=Course&loadLeftId=37&loadTopicId=39 66

1. What is the defining characteristic of prokaryotes? 2. What do eukaryotes have that prokaryotes lack? 3. What is the nucleoid region? 4. When did prokaryotes first appear?

Practice Answers

1. Prokaryotes refers to cells and organisms that lack a nucleus and specialized organelles. 2. Eukaryotes do have distinct nuclei and specialized membrane-bound organelles. 3. The nucleoid region is a concentrated region of nuclear (genetic) material in a prokaryotic cell. 4. Prokaryotes first appeared at least 3.5 billion years ago.

Review

1. What structures do prokaryotes use to move? 2. What is peptidoglycan, and how is it used to identify bacteria? 3. Describe prokaryotic cell shapes.

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Review Answers

1. Many prokaryotic cells possess a single or few flagellum, which assist with movement. 2. Peptidoglycans are made up of a sugar and an amino acid molecule complex that form a mesh-like layer within the cell wall, outside the cell membrane of bacteria. The amount of peptidoglycan in the cell wall differs between bacterial species. 3. Prokaryotes come in many different shapes, but the most common shapes are spheres (cocci), rods (bacilli), and helices (spirilla). Other prokaryote shapes include curved rods, long filaments, and even flat squares.

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1.4 Gram Stain Identification - Advanced

• Identify two ways of classifying prokaryotes based on their physical structure.

What’s with the cell wall? This represents what is known as a gram-positive cell wall, which has a very thick layer of peptidoglycan. Peptido- glycan is a polymer consisting of sugars and amino acids that forms the mesh-like cell wall layer. On the other hand, a gram-negative cell wall has just a thin layer of this substance.

Gram Stain Identification

While most bacterial cell walls contain peptidoglycan, not all bacterial cell walls have the same structure. There are two main types of bacterial cell walls: Gram positive and Gram negative, which are identified in a technique called the Gram stain, named after its developer, the Danish bacteriologist Hans Christian Gram. Gram-positive bacteria stain purple in the Gram staining procedure. Gram-negative bacteria stain red. Gram staining is one of the most useful staining procedures in traditional bacteriology. There are four basic steps to the Gram stain:

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1. Apply the first stain (a purple stain called crystal violet) to a heat-fixed smear of a bacterial culture. A heat- fixed smear is a drop of liquid containing bacterial cells that has been dried (fixed) to a glass slide by passing the slide quickly through the flame of a Bunsen burner. 2. Apply iodine on top of the crystal violet. The iodine acts as a fixative. 3. Wash the cells with alcohol or acetone. 4. Stain the cells again (counterstain) with a red dye, either safranin red or basic fuchsin.

FIGURE 1.6 The structure of the Gram positive and Gram negative cell walls. Gram positive cells stain bluish-purple, just as these Bacillus anthracis bacteria (the purple rods) have done. Gram negative cells are stained pinkish-red, like these Bacillus coagulans cells.

The Gram-Positive Cell Wall

The Gram-positive cell wall has a very thick peptidoglycan layer, which holds the crystal violet dye during the Gram staining procedure. The thick layer of peptidoglycan lies above the cell membrane. During Gram staining, iodine helps hold the crystal violet within the cells, and the alcohol/acetone wash that is carried out after application of that dye causes the peptidoglycan layer to shrink and trap the crystal violet dye inside the cells. As a result, Gram-positive bacteria appear purple, as shown in the Figure 1.6.

The Gram-Negative Cell Wall

Unlike the Gram positive cell wall, the Gram negative cell wall contains a thin peptidoglycan layer just above the cell membrane. In addition to the peptidoglycan layer, the Gram negative cell wall also has an outer phospholipid membrane. The outer membrane faces the outside environment. The thin peptidoglycan layer is sandwiched between two plasma membranes and does not hold onto the crystal violet stain during the Gram staining procedure. The second stain, safranin red, is taken up by the decolorized cells, so Gram negative bacteria appear red, as shown in the Figure 1.6. Archaea do not have peptidoglycan in their cell walls, so Gram staining is of limited use in identifying them. Many antibiotics act by stopping the production of peptidoglycan by the bacterium, thus killing the cell. Examples of antibiotics that inhibit peptidoglycan cross-links (bonds that link one peptidoglycan to another) in the cell wall

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include penicillins, such as ampicillin. The outer membrane of Gram negative cells can contain lipopolysaccharides. Lipopolysaccharides (also known as endotoxins) add strength to the structure of the Gram-negative cell and are sometimes toxic to the host.

Vocabulary

• Gram-negative bacteria: Bacteria that have a thin layer of peptidoglycan that is sandwiched between two lipid membranes; these bacteria stain pink in the Gram staining procedure.

• Gram-positive bacteria: Bacteria that have a thick layer of peptidoglycan; these bacteria stain purple in the Gram staining procedure.

• Gram stain: A method of differentiating bacterial species into two large groups based on the chemical and physical properties of their cell walls.

Summary

• Prokaryotes can be classified based on their shape and their Gram stain reaction. • However, the Gram stain is not a reliable method of identifying archaea, as they do not contain peptidoglycan in their cell walls.

Practice

Use this resource to answer the questions that follow.

• Gram Staining at http://serc.carleton.edu/microbelife/research_methods/microscopy/gramstain.html.

1. How does the gram stain discriminate between the two different categories of eubacteria? 2. What are the four chemicals used in the gram stain and what order are they used in? 3. Which category of bacteria retain the violet dye and which don’t? 4. What are the differences between gram-positive and gram-negative bacteria?

Practice Answers

1. The Gram stain procedure distinguishes between Gram positive and Gram negative groups by coloring these cells red or violet. Gram positive bacteria stain violet due to the presence of a thick layer of peptidoglycan in their cell walls, which retains the crystal violet these cells are stained with. Alternatively, Gram negative bacteria stain red, which is attributed to a thinner peptidoglycan wall, which does not retain the crystal violet during the decoloring process. 2. 1. crystal violet, 2. iodine solution, 3. decolorizer, 4. safranin 3. Gram positive bacteria (with a thicker peptidoglycan layer) retain crystal violet stain during the decolorization process, while Gram negative bacteria lose the crystal violet stain and are instead stained by the safranin in the final staining process. 4. Gram positive bacteria have a thick layer of peptidoglycan in their cell walls; Gram negative bacteria have a thinner peptidoglycan wall.

Review

1. What is Gram stain and why is it important? 2. How does the Gram stain work?

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Review Answers

1. Gram staining is used to differentiate the cell wall of bacteria. Gram-positive bacteria stain purple in the Gram staining procedure. Gram-negative bacteria stain red. 2. The size and composition of the cell wall determines the stain which is taken up by the cell wall.

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1.5 Prokaryote Intracellular Structures - Ad- vanced

• Identify structures unique to prokaryotic cells.

What’s inside a prokaryotic cell? A nucleus? Mitochondria? Endoplasmic Reticulum? No, no, and no. But there is a cytoskeleton. And it is made of proteins similar to those found in eukaryotes. Prokaryotic cytoskeletal elements play essential roles in protection and polarity determination.

Structures

Cytoplasm and Cytoskeleton

Cytoplasm is a jelly-like fluid that is found within the cell. The plasma membrane prevents the cytoplasm from leaking out of the cell. Prokaryotic cytoplasm holds the cell’s ribosomes, genetic material, and cytoskeleton in place. Cytoskeletons were once thought to be found only in eukaryotic cells, but scientists recently discovered that prokaryotes also have cytoskeletons. Recall that the cytoskeleton is a cellular scaffolding or skeleton contained within a cell’s cytoplasm. The prokaryotic cytoskeleton is composed of proteins similar to that of the eukaryotic cytoskeleton: actin and tubulin proteins. The prokaryotic cytoskeleton has many important roles in prokaryotes. Some of these roles include maintaining the cell’s shape and the movement of genetic material during cell division, as well as protection and polarity determination.

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Genetic Material

The genome of prokaryotes is usually a single loop of DNA, although there are some exceptions. Prokaryotes can also have small, self-replicating circular pieces of DNA called plasmids within their cells, as shown in the Figure 1.7. The DNA of prokaryotes is concentrated in an area called the nucleoid, where it is associated with ribosomes and other molecules. Unlike eukaryotic DNA, prokaryotic DNA is not enclosed within an organelle. The genes that are found on plasmids are genes that are not critical for general survival. In nature, they usually contain special genes that may give bacteria some type of advantage, such as antibiotic resistance, virulence, or gene transfer mechanisms. Plasmids are transferred between prokaryotes during conjugation. Prokaryotes also differ from eukaryotes in the structure, packing, density, and arrangement of genes on their genome. Prokaryotes have very compact genomes compared to eukaryotes. Only tRNA and rRNA bacterial genes have introns, which are non-coding regions between each gene. Introns are much more common in eukaryotic DNA. As discussed in the Protein Synthesis concepts, introns are removed during RNA processing.

FIGURE 1.7 The genetic material of a prokaryote. The bacterial DNA is concentrated in an area called the nucleoid.

Prokaryote genes are also expressed in groups, known as operons, instead of individually, as in eukaryotes. In a prokaryotic cell, all genes in an operon (three in the case of the well-characterized lac operon) are transcribed on the same piece of mRNA, so there is just one promoter, and then translated into separate proteins. If these genes were native to eukaryotes, they each would have their own promoter and be transcribed on their own strand of mRNA. To learn more about gene expression, see Concept Molecular Biology (Advanced).

Bacterial Microcompartments

Bacterial microcompartments are bacterial organelles that are made of interlocking proteins, forming a protein shell, located throughout the cytoplasm. These organelles do not contain lipids and are not surrounded by a phospholipid membrane. These organelles contain various enzymes. There are at least seven different types of bacterial microcompartments. Many are involved in metabolic pathways, including carboxysomes. Carboxysomes contain the enzymes RuBisCo and carbonic anhydrase and are found in carbon-fixing bacteria. RuBisCo is the most abundant enzyme on Earth. It is involved in the Calvin cycle of photosynthesis. See the Photosynthesis concepts for more information.

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Vocabulary

• bacterial microcompartment: Widespread bacterial organelles that are made of a protein shell that surrounds and encloses various enzymes.

• carboxysome: Bacterial microcompartments that contain enzymes involved in carbon fixation.

• cytoplasm: The gel-like material inside the plasma membrane of a cell.

• nucleoid: The area within the cytoplasm of a prokaryotic cell where the DNA is concentrated.

• operon: A region of prokaryotic DNA with a promoter, an operator, and one or more genes that encode proteins needed to perform a certain task.

• plasmid: A small circular piece of DNA that is physically separate from, and can replicate independently of, chromosomal DNA within a cell.

Summary

• The cytoplasm of a bacterial cell holds the cell’s ribosomes, genetic material, and cytoskeleton. • The bacterial genome is located in the nucleoid. The prokaryotic genome is one circular piece of DNA. Additional self-replicating plasmids are also often present. • Bacterial microcompartments are specific regions of the bacterial cell that can perform certain functions.

Practice

Use this resource to answer the questions that follow.

• Prokaryotic Cell Structure and Function at http://www.shmoop.com/biology-cells/prokaryotic-cells.html.

1. List the four main structures shared by all prokaryotic cells. 2. What is the difference between prokaryotic and eukaryotic cytoplasm. 3. Describe the role of the prokaryotic cytoskeleton. 4. Distinguish prokaryotic ribosomes from eukaryotic.

Practice Answers

1. The plasma membrane, cytoplasm, ribosomes, and genetic material (DNA and RNA). 2. Prokaryotic cytoplasm is very similar to the eukaryotic cytoplasm, except that it does not contain organelles. 3. The cytoskeleton is the framework along which particles in the cell, including proteins, ribosomes, and plasmids move around. 4. Prokaryotic ribosomes are smaller and have a slightly different shape and composition than those found in eukaryotic cells. Bacterial ribosomes have about half of the amount of rRNA and one third fewer ribosomal proteins than eukaryotic ribosomes have.

Review

1. Discuss the genetic material of prokaryotes. 2. What are bacterial microcompartments?

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Review Answers

1. The genome of prokaryotes is usually a single loop of DNA, although there are some exceptions. Prokaryotes can also have small, self-replicating circular plasmids. 2. Bacterial microcompartments are bacterial organelles that are made of interlocking proteins, forming a protein shell, located throughout the cytoplasm. These organelles do not contain lipids and are not surrounded by a phospholipid membrane. These organelles contain various enzymes.

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1.6 Prokaryote Extracellular Structures - Ad- vanced

• Identify structures unique to prokaryotic cells.

What does a snail leave in its tracks? A layer of slime. Bacteria also have a slime layer. The snail slime layer is one kind of mucus that is produced by the foot of the gastropod and is usually used for crawling on. The bacterial slime layer is an unorganized layer of extracellular material that surrounds bacteria cells, consisting mostly of exopolysaccharides, glycoproteins, and glycolipids.

Extracellular Structures

Prokaryotes need to sense and respond to their environment, in the same way that other living organisms do, so that they will survive and eventually reproduce. Examples of prokaryotic responses include moving toward food, away from toxins, and shutting down metabolic activity when environmental conditions become unfavorable. Prokaryotes have special cellular features that help them respond to their environment.

Capsule, Slime Layer, S-Layer

Many prokaryotic cells have an extra protective coating of polysaccharides that lies outside the cell wall. An outside layer that is well organized and is not easily washed off is called a capsule. An outside layer that is more disorganized and easily washed off is called a slime layer, shown in the Figure below. The functions of the capsule and slime layer include protecting the cell from environmental dangers, such as antibiotics, host immune systems, and drying out (see the DNA: The Hereditary Material (Advanced) concept). The capsule also allows bacteria to stick to surfaces and to each other. It may also allow bacterial colonies to survive chemical sterilization.

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FIGURE 1.8 Diagram of mucoid-like structures that prokaryotes can make to protect them- selves from environmental stresses. 1. Capsule 2. Slime layer 3. Biofilm. The formation of biofilms make infections diffi- cult to treat.

Biofilm

A biofilm is a complex grouping of microorganisms which secrete a sticky, protective coating that holds the prokaryotes together and to whatever surface they have colonized. Microorganisms within a biofilm are very resistant to antibiotics and other antimicrobial treatments. Biofilms, such as the one shown in the Figure 1.9, are now known to be a cause of chronic and recurring infections in people with cystic fibrosis or other chronic diseases. Biofilms are found everywhere there are prokaryotes: on the surface of rocks, leaves, inside water pipes, and even inside your mouth (dental plaque is a biofilm). Discoveries are still being made in this new area of research.

FIGURE 1.9 A S. aureus biofilm on the surface of a medical catheter that was removed from a patient. Although Staphylococcus can produce a capsule, as is shown here, cap- sule production is more common in other bacteria such as Klebsiella pneumoniae and Streptococcus pneumoniae.

An S-layer (surface layer) covers the entire cell and is commonly found in Gram positive bacteria, Gram negative bacteria, and archaea. It is made up of a layer of identical proteins or glycoproteins that have a tiled, floor-like pattern. The proteins and glycoproteins that make up the S-layer differ between species. The S-layer has many functions that vary from species to species. In some archaea, the S-layer is the only cell wall component and therefore is important for maintaining cell structure. An S-layer protects the cell against viruses and host immune responses. It also protects the cell from acidic conditions (low pH) and osmotic stress. Mutant bacteria that do not have an S-layer are more easily destroyed by immune cells and do not cause disease.

Fimbria

A fimbria (fimbriae, plural) is a short hair-like appendage that helps the prokaryotic cell “stick” to solid surfaces such as a rock or host tissue. Fimbriae are also called pili. Attachment to host surfaces is needed for colonization

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during infection or to make a biofilm. Prokaryotic cells can have many fimbriae, which are either located at the ends of a cell or spread over its entire surface. Mutant bacteria that do not have fimbriae cannot attach to their usual target surfaces and, thus, cannot cause disease. Fimbrae are used by some bacteria to glide about. A structure called a sex pilus attaches two prokaryotic cells and allows the transfer of plasmids between the cells.

Flagella

Flagella (flagellum, singular) are long, thin protein structures that stick out from the plasma membrane. Both eukaryotic and prokaryotic cells can have flagella. However, the structure and molecular make up of prokaryotic and eukaryotic flagella are very different. Flagella help prokaryotes move or swim towards food and away from toxins or repellents. Prokaryotic flagella are spiral-shaped and stiff. They can be located at one end of the cell, both ends of the cell, or all around the cell, as shown in the Figure 1.10. A prokaryotic cell can have one flagellum or many flagella. Flagella spin around a fixed base much like a spinning top. The corkscrew-type motion of the flagella cause the cell to move in a “roll and tumble” fashion.

FIGURE 1.10 Bacteria may have one (monotrichous), two, or many flagella that can be located at one or both ends of the cell or all around the cell (peritrichous). The flagella spin about in place, which causes the prokaryote to move in a tumbling motion. A micrograph of a Helicobacter pylori cell with many flagella is shown (bottom).

Endospores

Some prokaryotes form tough spores as a mechanism for survival, not reproduction. An endospore is a tough, non- reproductive structure made inside the cell of some species of bacteria. The main function of endospores is to ensure the survival of the DNA through stresses that would kill the cell. Endospores are resistant to ultraviolet and gamma radiation, drying, high temperature, starvation, and chemical disinfectants. Endospores are commonly found in soil and water, where they may survive for long periods of time. The position of the endospore within the cell differs among bacterial species and is useful in identification.

Vocabulary

• biofilm: A colony of prokaryotes that is stuck to a surface, such as a rock or a host’s tissue.

• capsule: A well-organized, extra protective coating of polysaccharides found in many prokaryotes that lies outside the cell wall.

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FIGURE 1.11 A preparation of Bacillus subtilis. Unfa- vorable conditions cause the B. subtilis cells to make spores within the cells. Clostridium tetani also are spore forming bacteria. C. tetani can survive for years in soil and cause tetanus if you step on something (or cut yourself) and they pen- etrate your skin.

• endospore: A tough, non-reproductive structure made inside the cell of some species of bacteria; the main function of endospores is to ensure the survival of the DNA through stresses that would kill the cell.

• fimbria (pl., fimbriae): A short, hair-like structure that helps prokaryotic cells stick to solid surfaces, such as a rock or host tissue; they are also known as a pili.

• flagella (singular, flagellum): A "tail-like" appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells; they are used for locomotion.

• pili: Hair-like structures on the surface of a prokaryotic cell that attach to other cells or surfaces; pili is another name for a fimbria.

• sex pilus: A hairlike appendage found on the surface of bacteria which allows for the exchange of genetic material.

• S-layer: The surface layer that covers the entire cell and is commonly found in Gram positive bacteria, Gram negative bacteria, and archaea; it is made up of a layer of identical proteins or glycoproteins.

• slime layer: A disorganized, easily washed off, extra protective coating of polysaccharides that lies outside the cell wall.

Summary

• Many prokaryotic cells have an extra protective coating of polysaccharides that lies outside the cell wall; this can be a capsule, slime layer, or S-layer. • Many prokaryotic organisms can form biofilms, a complex grouping of microorganisms with a protective coating that holds the prokaryotes together. • A fimbria is a short hair-like structure that helps the prokaryotic cell “stick” to solid surfaces. • Prokaryotes may have one or more flagella that provide locomotion. • Endospores may ensure the survival of bacterial DNA through harsh conditions.

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Practice

Use this resource to answer the questions that follow.

• Prokaryotic Cell Structure at http://www.ivyroses.com/Biology/Cells/Prokaryotic-Cell-Structure.php.

1. Describe bacterial capsule. 2. Describe the bacterial flagella. 3. What is ta sex pilus? 4. How is a mesosome similar to a cristae? 5. What does 70S and 80S designate?

Practice Answers

1. The outer layer of of prokaryotic cells is a gummy or slimy covering that may help bacteria stay together in colonies and/or provide some protection to the cell. 2. In many cases the bacterial flagellum is responsible for the motility, consuming energy in the process. The flagellum of a prokaryotic cell does not "beat" but rotates about a "bearing" in the cell wall - resulting in a "corkscrew" motion that drives the cell forwards in much the same way as a propeller propels some ships forward. 3. Some scientists prefer to reserve the word "pilus" for the appendage that is sometimes called the "sex pilus" because it participates in DNA transfer during bacterial conjugation - the bacterial equivalent of sexual reproduction or mating. 4. Both mesosomes and the cristae (folds of the inner-membrane) of mitochondria participate in the aerobic part of aerobic cellular respiration. 5. The smaller ribosomes in prokaryotic cells are the the 70S type, compared with the larger ribosomes in eukaryotic cells which are the 80S type.

Review

1. Describe the types of bacterial outer coverings. 2. What is a biofilm? 3. Describe the role of endospores. 4. Identify why the formation of endospores is not a form of reproduction.

Review Answers

1. An outside layer that is well organized and is not easily washed off is called a capsule. An outside layer that is more disorganized and easily washed off is called a slime layer. The functions of the capsule and slime layer include protecting the cell from environmental dangers, such as antibiotics, host immune systems, and drying out. The capsule also allows bacteria to stick to surfaces and to each other. It may also allow bacterial colonies to survive chemical sterilization. 2. A biofilm is a complex grouping of microorganisms which secrete a sticky, protective coating that holds the prokaryotes together and to whatever surface they have colonized. 3. The main function of endospores is to ensure the survival of the DNA through stresses that would kill the cell. 4. Endospores are tough spores used as a mechanism for survival, not reproduction.

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1.7 Introduction to Archaea - Advanced

• Identify places where archaea have been found.

What lives in here? Anything? Yes. The remarkable colors of geysers, like this one, come from the various life forms that live in them. Life in geysers come in the form of thermophilic prokaryotes - not bacteria, but archaea. No known eukaryotic organism can survive the harsh high temperature conditions of geysers.

Archaea

Archaea are prokaryotic organisms. They are exclusively single-celled organisms that lack nuclei. Archaea are similar to bacteria in much of their cell structure and metabolism. In fact, for many years scientists thought archaea were a type of bacteria that lived in extreme environments in which other bacteria would not survive. Even though they are both very small, archaea and bacteria are very different from one another. Archaea are now recognized as a distinct group of prokaryotes.

They are Archaea, Not Bacteria!

For archaea, the transcription and translation of their DNA and RNA—the processes that are involved in protein synthesis—are very similar to those of eukaryotes. Several other characteristics set the archaea apart from both bacteria and eukaryotes. Archaea have phospholipids in their cell membranes that are similar to both bacterial and eukaryotic phospholipids. However, many features of archaeal membrane lipids are unique to archaea. These differences may be an adaptation by some archaea for life in extreme environments. Although not unique, archaeal cell walls are unusual. The make up of arcaheal cell walls is very different from bacteria. Except for one group of methanogens (archaea that produce methane), archaea do not have peptidoglycan

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in their cell walls. The peptidoglycan in the methanogen cell wall is very different from the type found in bacteria. Archaea cells also have flagella that are very different in structure from bacterial flagella. Other differences between the domains are listed in the Table 1.1.

TABLE 1.1: Differences Between Archaea, Bacteria, and Eukaryotes

Structural/Genetic Differ- Archaea Bacteria Eukaryotes ence Cell Wall Most do not have peptido- Have peptidoglycan Do not have peptidogly- glycan can Cell Membrane Contains unusual phos- Unique to bacteria Unique to eukaryotes pholipids unlike bacterial phospholipids Flagella Flagella structure and Unique to bacteria Unique to eukaryotes how they function are very different from bacteria. Unique to archaea Genome Contains introns Contains very few introns Contains introns Ribosome Size 70S 70S 80S (mitochondria and (S refers to the unit of chloroplasts contain 70S measurement (the Sved- ribosomes) berg unit) - a measure of the rate of sedimentation in centrifugation.) Transcription and Similar to eukaryotes Unique to bacteria Translation

Extreme Life

FIGURE 1.12 A micrograph of a cluster of salt-loving (halophilic) archaea (left). These cells are about 5 µm long. Archaeal cells like these —confusingly called Halobacterium —live in salt ponds in San Francisco Bay, Cali- fornia. The salt concentration of the water in the salt ponds is higher than seawater. The water turns red from pigments made by halophilic archaea (right).

The environments in which archaea were first found are thought to be like the conditions on Earth millions of years ago. As a result, they were called archaebacteria (ancient bacteria). Such “ancient” conditions include extremes in temperature, extremes in acidity or alkalinity, high salt concentrations, and high pressure. Many archaea are found living in extreme conditions, and they are called extremophiles (“lovers” of extreme environments). Extremophiles that live in very salty conditions, like the Halobacteria shown in the Figure 1.12, are called extreme halophiles (extreme salt lovers). Methanogens (methane makers) are archaea that produce methane

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and are killed by exposure to oxygen. Methanogens have been found living in the oxygen-free mud of marshes, at the bottom of the ocean, and inside the digestive tracts of cows, termites, and marine life. Hyperthermophiles (high heat lovers) live in environments that are hotter than 80oC, such as in the waters of hot springs or geothermal pools. Astrobiology is the study of the possibility of life in space and on other planets. It is focused primarily on the study of the origin and evolution of life. Astrobiologists think that organisms similar to extremophiles may have developed on other planets, some of which (particularly Mars) are known to have conditions similar to those in which extremophile life is found on Earth.

FIGURE 1.13 Two extreme environments in which ar- chaea have been discovered. On the left is a black smoker, a type of hydrother- mal vent found on the ocean floor. The temperature of the water at the vent can reach 400oC and is extremely acidic, of- ten having a pH value as low as 2.8. On the right is an actively-venting cal- cium carbonate “beehive” chimney in the Lost City, a hydrothermal field in the mid- Atlantic ocean floor. These two types of hydrothermal vents are very different. The calcium carbonate chimney fluids are rich in methane and hydrogen, range in temperature from about 40oC to 90oC, and are very alkaline, with a pH of 9 to 11.

Scientists believe the first prokaryotes to evolve billions of years ago were hyperthermophiles that lived in environ- ments that were similar to hot springs or the deep-sea vents shown in the Figure 1.13. Archaea were originally thought to live only in extreme environments, but they have also been found in much milder conditions. Researchers have found archaea living among plankton on the ocean surface, in soil, in marshes, and even inside your body. Recently, several studies have shown that archaea exist at low temperatures as well. Methanogens have been found in low-temperature environments, such as cold, muddy sediments. Large numbers of archaea are found throughout most of the world’s oceans, a predominantly cold environment. Some studies of ocean waters have found that archaea are the most common form of life below a depth of 150 meters in the ocean.

The Role of Archaea in the Environment

Scientists still know relatively little about archaea. Very few archaea have grown sucessfully in the lab, so what the cells look like and how they metabolize nutrients is still largely unknown. The presence of the archaea in various environments has been determined by molecular analysis, detecting DNA sequences that are unique to the archaea. The role of archaea in geochemical cycles, such as the nitrogen cycle, phosphorus cycle, and carbon cycle, has yet to be discovered. One recent study has shown, however, that one group of marine archaea are able to carry out nitrification, a process that is important to the nitrogen cycle and a trait previously unknown among the archaea. Many methanogenic archaea are found in the digestive tracts of animals, such as cattle, termites, and humans. It is currently unclear if examples of archaeal pathogens exist, although a relationship has been proposed between the presence of some methanogens and human periodontal disease.

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The evolutionary relationship between Archaea and Eukarya remains an important problem. Many phylogenetic trees group the two together. The discovery of archaean-like genes in certain bacteria, such as Thermotoga, makes their relationship difficult to determine. Some have suggested that eukaryotes arose through the fusion of an archaeal cell and a bacterium, which then became the nucleus and cytoplasm. This idea accounts for various genetic similarities between eukaryotes and prokaryotes, but it does not explain much about differences in cell structure.

Vocabulary

• Archaea: A prokaryotic domain of microorganisms that resemble bacteria; most archaea live in extreme environments, such as around hydrothermal vents in the deep ocean, and are chemoautotrophs.

• extreme halophiles: Archaea that live in very salty conditions.

• extremophile: An organism that thrives in physically or geochemically extreme conditions that are detrimen- tal to most life on Earth.

• hyperthermophiles: High heat lovers; these are archaea that live in environments that are hotter than 80oC.

• methanogens: Archaea that produce methane and are killed by exposure to oxygen.

Summary

• Archaea are a distinct domain of prokaryotic organisms; they have distinct similarities, but also differences, with bacteria. • Archaea have distinct similarities to eukaryotic cells, suggesting that they are more closely related to eukary- otes than to bacteria. • Archaea were originally found in extreme environments but have since been found in seawater, soil, and even in the intestines and dental plaque of animals.

Practice

Use this resource to answer the questions that follow.

• Introduction to the Archaea at http://www.ucmp.berkeley.edu/archaea/archaea.html.

1. Why is the term Archaeabacteria incorrect? 2. Describe bacteriorhodopsin. 3. How were Archaea first identified?

Practice Answers

1. Although many books and articles still refer to these prokaryotes as "Archaebacteria", that term has been abandoned because they aren’t bacteria – they’re Archaea. 2. The light-sensitive pigment bacteriorhodopsin gives Halobacterium its color and provides it with chemical energy. Bacteriorhodopsin has a purple color, and it pumps protons to the outside of the membrane. When these protons flow back, they are used in the synthesis of ATP, which is the energy source of the cell. 3. While studying prokaryotic DNA relationships, Dr. Woese identified a group of "bacteria" (the Archaea) that lived at high temperatures or produced methane had DNA sequences that clustered together as a group, well away from the usual bacteria and the eukaryotes.

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Review

1. Discuss how archaea are distinct from bacteria. 2. Archaea are found only in extreme environments. Is this a true statement? Explain your answer.

Review Answers

1. Archaea have phospholipids in their cell membranes that are similar to both bacterial and eukaryotic phos- pholipids. The make up of arcaheal cell walls is very different from bacteria. Most archaea do not have peptidoglycan in their cell walls. Archaea cells also have flagella that are very different in structure from bacterial flagella. And the archaea genome contains introns. 2. Answers may vary. Yes, Archaea are found in extreme environments. But recently, archaea have been identified at low temperatures, which may also be considered an extreme environment. Large numbers of archaea are found throughout most of the world’s oceans, a predominantly cold environment.

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1.8 Introduction to Bacteria - Advanced

• Identify types of bacteria.

What likes to live in your gut? This rendering represents the bacteria Escherichia coli. E. coli is a Gram-negative, facultative anaerobic, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms.

Bacteria

Bacteria are the prokaryotes that are most familiar to you, and the majority of known prokaryotes are bacteria. They are the most diverse and abundant group of organisms on Earth. Bacteria inhabit almost all environments where some liquid water is available and the temperature is below 140°C. They are found in sea water, soil, animal’s intestines, hot springs, and even in rocks deep beneath the Earth’s crust. Practically all surfaces which have not been specially sterilized are covered in bacteria. The number of bacteria in the world is estimated to be around five million trillion trillion, or 5 × 1030. There are many thousands of known bacterial species, and many more are known to exist. Scientists estimate that we have been able to grow only about one percent of all bacterial species in the lab. Nonetheless, every major mode of obtaining nutrition is represented by the known species of bacteria. In a similar way to the archaea, bacteria are classified into large groups based on their biochemical and evolutionary relationships. Some of these groups are discussed below.

Proteobacteria

The Proteobacteria is a large and very diverse phylum of Gram negative bacteria that have a variety of ways of getting food. Proteobacteria come in many different shapes, including cocci, bacilli, and spirilla. The phylum is named after the ancient Greek god Proteus, who could change his shape. The largest bacterial species known, Thiomargarita namibiensis, belongs to the phylum proteobacteria.

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The proteobacteria are grouped mostly by similarities in their rRNA gene sequences. The group includes a wide variety of pathogens, such as members of the genera Salmonella and Helicobacter. Photosynthetic bacteria known as purple bacteria are members of this group. Others are free-living and include many of the bacteria responsible for nitrogen fixation, such as bacteria of the genus Rhizobium. Nitrogen-fixing bacteria are important to many ecosystems because they take elemental nitrogen (N2) from the atmosphere and change it into a form (nitrate or − NO3 ) that can be used by plants and animals. Nitrogen is an important element for making proteins, DNA, and RNA. Other species in this group, such as Escherichia coli, live in the intestines of animals, including humans. Bdellovibrio are proteobacteria that eat other bacteria. A Bdellovibrio cell attacks other Gram-negative bacteria by crashing into them at speeds of up to 160 µm per second, which is over 100 times their length per second! Once attached to the prey cell, the Bdellovibrio cell “drills” into the prey cell and digests its insides.

Chlamydiae

The Chlamydiae is a phylum of Gram-negative bacteria that live only inside other cells (known as obligate intracel- lular pathogens). They are as small or even smaller than many viruses. Chlamydiae depend on the host cell for all its nutrient needs and do not grow outside the host cell. As a result, chlamydiae cannot be grown on artificial media. Many chlamydiae live in a non-infectious state within specific hosts. Scientists believe that these hosts provide a natural reservoir for these species. Chlamydia trachomatis is the causative agent of chlamydia, the most common sexually transmitted infection in people worldwide.

Spirochetes

The Spirochetes are a phylum of distinctive Gram-negative, long, spiral-shaped bacteria. Spirochetes are distin- guished from other bacterial phyla by the presence of flagella running lengthwise between the cell membrane and outer membrane. These flagella cause a twisting motion which allows the spirochete to move about. Most spirochetes are free-living and anaerobic, but many spirochetes cause diseases. Examples include Borrelia burgdorferi, which causes Lyme disease (shown in the Figure 1.14), and Treponema pallidum, which causes syphilis.

FIGURE 1.14 Borrelia burgdorferi, the bacteria that cause Lyme disease.

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Gram-Positive Bacteria

Gram-positive bacteria make up a very large, diverse group of bacteria. Gram positive bacteria are divided into two groups based on the guanine and cytosine content of their DNA: one group has a low G and C content, the other group has a high G and C content. Actinobacteria are Gram positive bacteria that form branching colonies. Streptomyces bacteria are a type of Actinobacteria. Streptomycetes are found mostly in soil and in decaying vegetation, and most produce spores. They also produce chemicals that inhibit the growth of or kill other microorganisms in the soil. Streptomycin, actinomycin, and neomycin are antibiotic medicines that are made from Streptomycetes antibiotic compounds. Other Gram positive bacteria include nitrogen-fixing bacteria of the genus Frankia, which live in root nodules in plant roots, and members of the genus Mycobacterium, shown in the Figure 1.15, which cause the diseases leprosy (Hansen’s disease) and tuberculosis (TB).

FIGURE 1.15 Mycobacteria. Under a high magnification of 15549x, this scanning electron micro- graph (SEM) shows the structure of a number of Gram-positive Mycobacterium tuberculosis bacteria. M. tuberculosis causes TB (tuberculosis). As an obligate aerobic organism, M. tuberculosis can only survive in an environment that has oxygen.

Cyanobacteria

Cyanobacteria get their energy by photosynthesis. The name "cyanobacteria" comes from the color of the bacteria —cyan, a bluish green color, as shown in the Figure 1.16. Cyanobacteria used to be called blue-green algae, because scientists once thought they were algae, not prokaryotes. Cyanobacteria are very numerous and are important producers of oxygen in marine and freshwater ecosystems. They are also an important part of the marine nitrogen cycle. Stromatolites are hardened, sedimentary formations that are believed to have been made by the binding and cement- ing of grains of sand by ancient cyanobacteria. Cyanobacteria use water, carbon dioxide, and sunlight to create their food. The byproducts of this process are oxygen and calcium carbonate (lime). A layer of mucous often forms over mats of cyanobacterial cells. In modern microbial mats, debris from the surrounding habitat can become trapped within the mucous, which can be cemented together by the calcium carbonate to grow thin laminations of limestone. These laminations can build up over time, resulting in the banded pattern common to stromatolites. Fossilized stromatolites, shown in the Figure 1.17 are believed to have been made by the binding and cementing of grains of sand by ancient cyanobacteria. Recently, fossilized stromatolites that are about 3.4 billion years old were discovered. Some scientists think that ancient cyanobacteria made these stromatolites, the same cyanobacteria that were responsible for releasing the oxygen that made the early oxygen-rich atmosphere. The increase in oxygen levels dramatically changed the life forms on Earth and lead to an explosion of biodiversity. See the Fossil Museum

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FIGURE 1.16 Anabaena is a species of filamentous cyanobacterium (bottom). It is known for its nitrogen fixing abilities. The bacte- rial cells attach to each other, forming a “string of beads.” The large cell on the left side of the chain fixes nitrogen. Anabaena organisms also form symbiotic relation- ships with certain plants.

web site for further information: http://www.fossilmuseum.net/Tree_of_Life/Stromatolites.htm.

FIGURE 1.17 (Left) Fossil stromatolites in the Siyeh For- mation, Glacier National Park, Montana may have been created by cyanobacteria. (Right) Modern stromatolites are mostly found in hypersaline lakes and marine lagoons where extreme conditions do not allow for animal grazing. One such loca- tion is Hamelin Pool Marine Nature Re- serve, Shark Bay in Western Australia.

Vocabulary

• chlamydiae: A phylum of Gram-negative bacteria that live only inside other cells (obligate intracellular pathogens).

• cyanobacteria: A phylum of bacteria that obtain their energy through photosynthesis; they are also known as blue-green bacteria or blue-green algae.

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• Gram-positive bacteria: Bacteria that have a thick layer of peptidoglycan; they stain purple in the Gram staining procedure.

• proteobacteria: A large and very diverse phylum of Gram negative bacteria that have a variety of ways of getting food.

• spirochetes: A phylum of distinctive Gram-negative, long, spiral-shaped bacteria.

• stromatolites: Structures formed in shallow water by the trapping, binding, and cementation of biofilms of microorganisms, especially cyanobacteria.

Summary

• Bacteria are the more common forms of prokaryotic organisms. • Every known mode of obtaining nutrition is represented in bacteria. • Bacteria are classified into large groups based on their biochemical and evolutionary relationships.

Practice

Use this resource to answer the questions that follow.

• Bacteria at http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria.

1. What may be an advantage of a plasmid? 2. What is the role of bacterial that live in soil or dead plant matter? 3. Describe the bacterial reproduction process. 4. What are bacterial endospores?

Practice Answers

1. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example, it may contain a gene that makes the bacterium resistant to a certain antibiotic. 2. Some bacteria live in the soil or on dead plant matter where they play an important role in the cycling of nutrients. 3. Binary fission, the process of bacterial reproduction, 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. 4. Bacterial endospores are dormant structures, which are extremely resistant to hostile physical and chemical conditions such as heat, UV radiation and disinfectants. This makes destroying them very difficult.

Review

1. You are given a sample of an unknown bacterium. How would you narrow down what type of bacterium it could be?

Review Answers

1. Answers may vary. Answers may include examining the bacterium under a microscope.

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1.9 Prokaryote Nutrition and Metabolism - Ad- vanced

• Outline how prokaryotes can be classified based on their nutritional needs.

Is this considered nutrition? You obviously get your energy from eating, although ice cream may not be that nutritious (but it sure tastes good). What happens if you can’t digest the lactose in dairy products like this ice cream? Bacteria in your colon can metabolize the lactose for you, although there are some side effects.

Nutrition and Metabolism of Prokaryotes

Prokaryotic metabolism refers to the ways prokaryotes obtain the energy and nutrients they need to live and reproduce. Prokaryotic species can be classified based on how they get the nutrients they need to survive. However, classifications based on metabolism often do not correspond with modern genetic classifications. The nutritional needs of a prokaryote are major factors in determining the prokaryote’s ecological niche. These nutritional needs may determine the role of a prokaryotic organism in biogeochemical cycles. Special nutritional needs often allow for certain prokaryotes to also be used in industrial processes.

Classification of Prokaryotes Based on Metabolism

Two major nutritional needs can be used to group prokaryotes. These are (1) carbon metabolism - their source of carbon for building organic molecules within the cells and (2) energy metabolism - their source of energy used for growth. In terms of carbon metabolism, prokaryotes are classified as either heterotrophic or autotrophic:

• Heterotrophic organisms use organic compounds —usually from other organisms —as carbon sources.

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• Autotrophic organisms use carbon dioxide (CO2) as their only or main source of carbon. Many autotrophic bacteria are photosynthetic and get their carbon from the carbon dioxide in the atmosphere.

Energy metabolism in prokaryotes is classified as one of the following:

• Phototrophic organisms capture light energy from the sun and convert it into chemical energy inside their cells. • Chemotrophic organisms break down either organic or inorganic molecules to supply energy for the cell. Some chemotrophic organisms can also use their organic energy-supplying molecules as a carbon supply, which would make them chemoheterotrophs. • Photoheterotrophs are organisms that capture light energy to convert to chemical energy in the cells, but they get carbon from organic sources (other organisms). Examples are purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. • Chemoheterotrophs are organisms that get their energy source and carbon source from organic sources. Chemoheterotrophs must consume organic building blocks that they are unable to make themselves. Most get their energy from organic molecules such as sugars. This mode of obtaining nutrition is very common among eukaryotes, including humans. • Photoautotrophs are organisms that capture light energy and use carbon dioxide as their carbon source. There are many photoautotrophic prokaryotes, including cyanobacteria. Photoautotrophic prokaryotes use similar compounds to those of plants to trap light energy. • Chemoautotrophs are organisms that break down inorganic molecules to supply energy for the cell and use carbon dioxide as a carbon source. Chemoautotrophs include prokaryotes that break down hydrogen sulfide (H2S the “rotten egg” smelling gas) and ammonia (NH4). Nitrosomonas, a species of soil bacterium, oxidize + − NH4 to nitrite (NO2 ). This reaction releases energy that the bacteria use. Many chemoautotrophs also live in extreme environments, such as deep sea vents.

The Figure 1.18 illustrates how to group a given prokaryote based on its metabolic type.

FIGURE 1.18 This flowchart helps to determine if a species is an autotroph or a heterotroph and whether it is a phototroph or a chemotroph. For example, “Carbon obtained from elsewhere?” asks if the source of carbon is another organism. If the answer is “yes,” the organism is heterotrophic. If the answer is “no,” the organisms is autotrophic.

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Chemoheterotrophs

Most microbes are chemoheterotrophic; they use organic compounds as both carbon and energy sources. Het- erotrophic microbes live off of nutrients that they take from living hosts or find in dead organic matter. Microbial metabolism is the main reason for the decomposition of dead organisms. Without prokaryotic decomposition, many biogeochemical cycles, such as the carbon cycle and the nitrogen cycle, could not occur. The remains of dead organisms would litter the planet, and the nutrients within them would be unavailable for other organisms to use. Pathogenic (disease-causing) prokaryotes are heterotrophic, as they are predators or parasites of other organisms. Bacteria of the species Bdellovibrio are predators and intracellular parasites of other bacteria. Bdellovibrio bacteria are chemoheterotrophs.

Autotrophs

Most photosynthetic microbes are autotrophs; they use inorganic cabon (carbon dioxide) as a carbon source. Some photosynthetic bacteria are photoheterotrophs, meaning that they use organic carbon compounds as a carbon source for growth. Some photosynthetic organisms also fix nitrogen. To learn more about photosynthesis, see the Photo- synthesis concepts. Prokaryotes such as cyanobacteria that harvest energy from the sun for photosynthesis are photoautotrophs. Chemoau- totrophs oxidize inorganic molecules to get energy. For example, a species of nitrifiying soil bacteria called Nitro- + − somonas oxidize NH4 to nitrite (NO2 ). This reaction releases energy that the bacteria can use. Nitrosomonas bacteria and other nitrifying prokaryotes are very important to the nitrogen cycle. Nitrogen fixation by bacteria also benefits other organisms. Nitrogen is an element needed for growth by all organisms. While extremely common (about 80 percent by volume) in the atmosphere, nitrogen gas (N2) cannot be used by most organisms. The role of prokaryotes in the nitrogen cycle is shown in the Figure 1.19.

FIGURE 1.19 Throughout all of nature, only special- ized bacteria are able to fix nitrogen gas from the air. They convert nitrogen gas (N2) into ammonia (NH3), which is eas- ily used by all organisms. These bac- teria, therefore, are very important eco- logically and are often essential for the survival of entire ecosystems. This is es- pecially true in the ocean, where nitrogen- fixing cyanobacteria are often the only sources of fixed nitrogen, and in soils, where specialized symbioses exist be- tween legumes and their nitrogen-fixing partners to provide the nitrogen needed by these plants for growth and repair.

Vocabulary

• autotrophic organisms: An organism capable of transforming one form of energy –usually light –into the food, or stored chemical energy, they need to do work; they are also known as producers.

39 1.9. Prokaryote Nutrition and Metabolism - Advanced www.ck12.org

• chemoautotrophs: Organisms that use the energy stored in chemical compounds to make organic molecules by chemosynthesis.

• chemoheterotrophs: Organisms that use organic compounds as both carbon and energy sources; they must consume organic building blocks.

• chemotrophic organisms: Organisms that break down either organic or inorganic molecules to supply energy for the cell.

• heterotrophic organisms: Organisms that use organic compounds —usually from other organisms —as carbon sources; these organisms must consume organic molecules; they are consumers.

• photoautotrophs: Organisms that capture light energy and use carbon dioxide as their carbon source; plants, algae, and certain bacteria are photoautotrophs.

• photoheterotrophs: Organisms that capture light energy to convert to chemical energy in the cells, but obtain their carbon from organic sources.

• phototrophic organisms: Organisms that capture light energy from the sun and convert it into chemical energy inside their cell.

• prokaryotic metabolism: Refers to the various ways prokaryotes get the energy and nutrients they needs to live and reproduce.

Summary

• Prokaryotic metabolism refers to the ways prokaryotes obtain the energy and nutrients they need to live and reproduce. • Every known mode of nutrition is observed in prokaryotes. • Prokaryotes can be classified based on their sources of carbon (heterotrophy or autotrophy) and energy (chemotrophy or phototrophy). • Prokaryotes are very important in the nitrogen cycle; they convert nitrogen gas into ammonia, a source of nitrogen that plants can use.

Practice

Use this resource to answer the questions that follow.

• Prokaryotic Metabolism at http://www.cliffsnotes.com/sciences/biology/plant-biology/prokaryotes-and-viruse s/prokaryote-metabolism.

Practice Answers

Review

1. How are prokaryotes classified based on their carbon and energy metabolisms? 2. Outline the role of prokaryotes in the nitrogen cycle. 3. What might happen if nitrogen bacteria were to suddenly disappear?

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Review Answers

1. For carbon metabolisms, they can be heterotrophs, which use organic carbon as their source of carbon, or autotrophs, which only use carbon dioxide.. For energy metabolisms, they can be phototrophic, which capture energy from the sun, or chemotrophic, which break down molecules for energy. + − 2. Prokaryotes convert nitrogen gas in the atmosphere (N2) to ammonium NH4 , nitrite (NO2 ), and nitrate − (NO3 ). 3. If nitrogen bacteria disappeared, all the plants in the world would die, and the ecosystem would collapse.

41 1.10. Prokaryote Habitats - Advanced www.ck12.org

1.10 Prokaryote Habitats - Advanced

• Identify prokaryotic habitats.

What would want to live here? This is a volcanic hot spring in Rotorua, New Zealand. The city is known for its geothermal activity and features geysers and hot mud pools. Rotorua has the nickname Sulfur City, because of the hydrogen sulfide emissions which give the whole city a "rotten egg" smell. What likes to live in these hot springs? Archaea, of course.

Prokaryote Habitats

Prokaryotes have a wide range of metabolisms. They live in a particular habitat because they are able to “eat” whatever is around them. For example, there are bacteria and archaea that break down hydrogen sulfide to produce ATP. Hydrogen sulfide is the gas that gives both rotten eggs and sewage their distinctive smell. It is poisonous to animals, but some prokaryotes depend on it for life. Organisms that are obligate aerobes need oxygen to live. That is, they use oxygen as a terminal electron acceptor while making ATP (see the Cellular Respiration concepts). Humans are obligate aerobes and so are Mycobacterium tuberculosis bacteria. M. tuberculosis causes tuberculosis (TB). Obligate aerobes are found only in places with molecular oxygen. An anaerobic organism is any organism that does not need oxygen for growth and even dies in its presence. Obligate anaerobes will die when exposed to atmospheric levels of oxygen. Clostridium perfringens bacteria, which are commonly found in soil around the world, are obligate anaerobes. Infection of a wound by C. perfringens bacteria causes the disease gas gangrene. Obligate anaerobes use molecules other than oxygen as terminal electron acceptors. Facultative anaerobic organisms, which are usually prokaryotic, make ATP by aerobic respiration if oxygen is present, but can also survive without oxygen. In the absence of oxygen, they switch to the process of fermentation to make ATP. Fermentation is a type of heterotrophic metabolism that uses organic carbon instead of oxygen as a terminal electron acceptor. Examples of facultative anaerobic bacteria are the Staphylococci species, Escherichia

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coli, Corynebacterium species, and Listeria species. Many bacteria that cause human diseases are faculatively anaerobic. Fermentative organisms are very important industrially and are used to make many different types of food products. The different metabolic end products produced by each specific bacterial species are responsible for the different tastes and properties of each food.

Optimum Temperatures

Just like you, prokaryotes live and grow best within certain temperature ranges. Scientists can classify prokaryotes by their temperature preferences. Thermophiles live at relatively high temperatures, above 45oC (113oF). Thermophiles are found in geothermally heated regions of the Earth, such as deep sea hydrothermal vents and hot springs, like the Morning Glory pool in Yellowstone National Park, shown in the Figure 1.20. Some thermophiles live in decaying plant matter, such as peat bogs and compost. Many thermophiles are archaea. Extreme thermophiles (or hyperthermophiles) live in temperatures hotter than 80oC (176oF).

FIGURE 1.20 The Morning Glory pool of Yellowstone National Park in the United States is a geothermal pool whose waters are heated to high temperatures by magma deep underground. Hyperthermophilic organ- isms, such as members of the archaeal genus Sulfolobus, can live at tempera- tures between 60-80oC and a pH of 3.

Thermophiles have enzymes that can function at high temperatures. Some of these enzymes have industrial ap- plications. Some are used in molecular biology (for example heat-stable DNA polymerases for polymerase chain reaction), and enzymes are added to washing detergents to help remove stains. Psychrophiles grow and reproduce in cold temperatures. The optimal growth temperature of some psychrophiles is 15oC or lower; they cannot grow in temperatures above 20oC. Other psychrophiles may grow in a temperature range from 0oC to about 40oC (32oF to 104oF). The environments that psychrophiles inhabit are found all around Earth. A large fraction of the planet’s surface (including the sea floor) has temperatures lower than 15oC. Psychrophiles live in such places as permafrost soils, deep-ocean waters, and both Arctic and Antarctic glaciers and snowfields. Mesophiles grow best in moderate temperature, typically between 25oC and 40oC (77oF and 104oF). Mesophiles are often found living in or on the bodies of humans or other animals. The optimal growth temperature of many pathogenic mesophiles is 37oC (98oF), the normal human body temperature. Mesophilic organisms have important uses in food preparation, including cheese, yogurt, beer, and wine.

43 1.10. Prokaryote Habitats - Advanced www.ck12.org

Vocabulary

• anaerobic organism: Any organism that does not need oxygen to produce ATP and may even die in an aerobic environment.

• facultative anaerobic organism: An organism which can respire aerobically when oxygen is present, but is also capable of fermentation when oxygen levels are low.

• fermentation: A type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic acid to one or more other compounds and the formation of NAD+; the process of producing ATP in the absence of oxygen through glycolysis.

• mesophile: Prokaryotic organism that grows best in moderate temperature, typically between 25oC and 40oC (77oF and 104oF).

• obligate aerobe: An organism which requires oxygen for cellular respiration.

• obligate anaerobe: An organism which uses anaerobic respiration and dies in the presence of oxygen.

• psychrophile: A prokaryotic organism that grows and reproduces in cold temperatures.

• thermophile: A prokaryotic organism that lives at relatively high temperatures, above 45oC (113oF).

Summary

• Aerobic prokaryotes live in habitats with oxygen. • Anaerobic prokaryotes live in habitats without oxygen. • Prokaryotes may also be adapted to habitats that are hot, moderate, or cold in temperature.

Practice

Use this resource to answer the questions that follow.

• Prokaryotes and harsh environments at https://www.boundless.com/biology/prokaryotes/prokaryotes-can- adapt-well-to-their-environment/prokaryotes-and-harsh-environments/.

Practice Answers

Review

1. Apply lesson concepts to explain why many prokaryotes are adapted for living at the normal internal temper- ature of the human body. 2. Compare psychrophiles to thermophiles and mesophiles. 3. What are facultative anaerobic organisms? Give an example.

44 www.ck12.org Chapter 1. Microbiology - Advanced

Review Answers

1. These prokaryotes are mesophiles, so they grow best at the temperature of the human body. 2. Psychrophiles are adapted for living in cold environments, thermophiles are adapted for living in hot environ- ments, and mesophiles are adapted for warm environments. 3. Facultative anaerobic organisms are those that cannot survive in oxygen, such as Clostridium perfringens.

45 1.11. Prokaryote Growth and Reproduction - Advanced www.ck12.org

1.11 Prokaryote Growth and Reproduction - Ad- vanced

• Summarize the process of prokaryotic reproduction. • Outline the process of genetic transfer in prokaryotes.

Are all these bacteria the same? A plate of streaked bacteria usually starts from the same colony. The bacteria grow and reproduce, producing billions of genetically identical cells. So yes, all these bacteria are the same.

Growth and Reproduction of Prokaryotes

Unlike multicellular organisms, an increase in the size of a prokaryote (cell growth) is tightly linked to reproduction by cell division. Prokaryotes grow to a fixed size and then reproduce through binary fission.

Binary Fission

Binary fission is a form of asexual reproduction in which one cell divides to produce two identical daughter cells. Asexual reproduction differs from sexual reproduction in that it does not involve meiosis or fertilization of gametes. This process will eventually produce many millions of identical cells. Binary fission is shown in the Figure 1.21. Under optimal conditions, bacteria can grow and divide rapidly, and some bacterial populations can double as quickly as every 20 minutes. Some prokaryotes can form more complex reproductive structures that allow for the dispersal

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of the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and arial hyphae formation by Streptomyces.

FIGURE 1.21 A schematic diagram of cellular growth (elongation) and binary fission of bacilli. Blue and red lines indicate old and newly- synthesized portions of the bacterial cell wall respectively. The DNA inside the bacterium is copied, and the daughter cells receive an exact copy of the parental DNA. Fission involves a cytoskeletal pro- tein, FtsZ, that forms a ring at the site of cell division.

Genetic Transfer

Prokaryotes can also “grab” pieces of DNA from their environment and exchange DNA with other microbes. There are three main ways that DNA can be exchanged: conjugation, transformation, and transduction. Bacterial conjugation is the transfer of genetic material between bacteria by direct cell-to-cell contact. The donor cell makes a structure called an F pilus, or sex pilus. The F pilus attaches one cell to another cell. The membranes of the two cells merge and genetic material, usually a plasmid, moves into the recipient cell, as shown in the Figure 1.22. Transduction is the process by which prokaryotic DNA is moved from one prokaryote to another by a virus. When a phage (viruses that infect prokaryotes) infects a cell, the phage reproduces by “hijacking” the DNA replication machinery of the host cell to make many copies of their own DNA or RNA. The host cell also transcribes and translates the phage genes. The new copies of phage DNA or RNA are then packaged into newly made phages. Sometimes, small pieces of prokaryotic DNA, rather than the phage genome, are packed into the phage. At the same

47 1.11. Prokaryote Growth and Reproduction - Advanced www.ck12.org

FIGURE 1.22 A flowchart showing bacterial conjuga- tion.

time, some phage genes are left behind in the prokaryotic chromosome. These prokaryotic genes are then transferred to other prokaryotes by the new phage. Bacterial transformation is the process by which bacterial cells take up naked DNA molecules from their envi- ronment. This process is used extensively in biotechnology (see the Concept Biotechnology (Advanced)). Artificial transformation and transduction are used in research and technology labs to transfer genes between prokaryotes, viruses, and eukaryotes. It is a useful way to investigate the functions of genes, study genetic diseases, and to develop transgenic organisms that can give valuable scientific information, as well as make medicines or other useful compounds. A bacterial artificial chromosome (BAC) is an artificial plasmid that is used in the genetic engineering of bacteria, usually E. coli. BACs are similar to a type of plasmid that is naturally found in some bacteria. BACs are often used in genome projects, including the Human Genome Project, to sequence the genetic code of organisms. A short piece of the organism’s DNA is copied many times after it is inserted into a BAC. Making many copies of the DNA fragment makes it easier for scientists to sequence the DNA fragment. Finally, the sequenced fragments are ordered based on overlapping sequences, much like a jigsaw puzzle, and scientists can then “read” the genomic sequence of the organism. The Human Genome Project and genetic engineering are discussed in the Concept Biotechnology (Advanced).

Growing Bacteria in the Lab

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as nutrient agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when

48 www.ck12.org Chapter 1. Microbiology - Advanced

measurement of growth or large volumes of cells are required.

FIGURE 1.23 Left, a solid agar plate with prokary- ote colonies. These microorganisms were isolated from a deep-water sponge. Right, E. coli bacteria replicate to form a larger mass of identical cells. Other prokaryotes, including the ones shown in the agar plate here, replicate in a similar way. Eventually, so many bacteria will be produced that the colony will become visible, just as the colonies in the agar plate are visible.

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. A solid agar culture plate is shown in the Figure 1.23. Prokaryotes rarely grow and reproduce so quickly in nature, because nutrients are limited in natural environments. Prokaryotes grow slowly and do not reproduce indefinitely. But, some prokaryotes can grow very rapidly when nutrients become available, even for a short period of time. An example of such a population explosion is the formation of cyanobacterial blooms that can occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Strepto- myces bacteria. These antibiotics inhibit the growth of competing microorganisms. In nature, many prokaryotes live in groups called biofilms. Biofilms may allow for increased supply of nutrients and protection from environmental stresses.

Vocabulary

• bacterial artificial chromosome (BAC): An artificial plasmid that is used in the genetic engineering of bacteria, usually E. coli.

• bacterial conjugation: The transfer of genetic material between bacteria by direct cell-to-cell contact.

• bacterial transformation: The process by which bacterial cells take up naked DNA molecules from their environment.

• binary fission: Asexual reproduction in prokaryotic organisms, which produces two identical cells.

• transduction: The process by which prokaryotic DNA is moved from one prokaryote to another by a virus.

Summary

• Binary fission is a form of asexual reproduction in which one cell divides to produce two identical daughter cells. Asexual reproduction differs from sexual reproduction in that it does not involve meiosis or fertilization of gametes. This process will eventually produce many millions of identical cells.

49 1.11. Prokaryote Growth and Reproduction - Advanced www.ck12.org

• Forms of genetic transfer include conjugation, in which there is a transfer of genetic material between bac- teria by direct cell-to-cell contact, transformation, the process by which bacterial cells take up naked DNA molecules from their environment, and transduction, the process by which bacterial DNA is moved from one bacterium to another by a virus.

Practice

Use this resource to answer the questions that follow.

• Binary Fission of Prokaryotic Cells at http://www.scienceprofonline.com/microbiology/binary-fission-cel l-division-reproduction-prokaryotes.html.

Practice Answers

Review

1. What is binary fission? 2. What happens during binary fission? 3. Outline the process of transduction. 4. Why might genetic transfer be important for the survival of prokaryote species? 5. Why might genetic transfer make genetic comparisons of prokaryotes difficult to interpret in studies of their evolution?

Review Answers

1. Binary fission is when one cell divides to form two new cells. 2. During binary fission, the DNA is copied. The cell then divides in two, leaving one copy of DNA in each cell. 3. During transduction, a virus infects a prokaryote and changes its DNA. 4. Genetic transfer helps increase genetic variety, which allows the prokaryotes to more easily adapt to different environments. 5. Since genetic transfer occurs, two bacteria that are not very evolutionary close could have the same DNA.

50 www.ck12.org Chapter 1. Microbiology - Advanced

1.12 Symbiotic Relationships of Prokaryotes - Advanced

• Outline the types of relationships that prokaryotes can have with other organisms.

Do you want to keep all bacteria away? The human body can be described as a social network —containing trillions of bacteria and other microorganisms that inhabit our skin, genital areas, mouth, and especially intestines. In fact, most of the cells in the human body are not human at all. Bacterial cells in the human body outnumber human cells 10 to one. And they do this to help us and themselves.

Symbiotic Relationships

Biological interactions result when organisms in an ecosystem interact with each other. In the natural world, no organism is isolated from its surroundings. It is a part of its environment, which is rich in living organisms and non-living factors. All of these living and non-living elements interact with each other in some way. An organism’s interactions with its environment are necessary for both the survival of that organism and the functioning of the ecosystem as a whole. Despite their tiny size, prokaryotes can form close relationships with other organisms, such as the cow and calf shown in the Figure 1.24. Usually bacteria live on or in other organisms - their host. These symbiotic relationships can be classified based on whether the host is helped, harmed, or not affected by the microorganisms. Such relationships are respectively classified as mutualistic, parasitic, and commensal.

Mutualism

Mutualism is a biological interaction between individuals of two different species, where both individuals derive a fitness benefit: for example, increased survivorship. Similar interactions within a single species are known as

51 1.12. Symbiotic Relationships of Prokaryotes - Advanced www.ck12.org

FIGURE 1.24 Even though cattle eat mostly grass, they do not have the enzymes to digest the cellulose in the grass. Cellulose is an important carbohydrate that makes up the cell wall of plant cells. Instead, bacteria and other microorganisms in the stomach of cattle break down the cellulose into a form that cattle can absorb and use.

co-operation. Mutualistic interactions can be thought of as a form of trade, in which species trade resources (for example, nutrients), offspring dispersal, or protection from predators. Bacteria and archaea living in the gut of different animals have mutualistic relationships with their hosts. The prokaryotes carry out a number of useful jobs for humans and other animals, including digestion of unused nutrients, synthesis of vitamins (such as folic acid, vitamin K, and biotin), preventing the growth of harmful microorganisms, training the immune system to respond only to pathogens, and defending against some diseases. Mutualistic bacteria in your intestines can help protect you against infection by pathogenic bacteria. For example, gut bacteria prevent the growth of pathogenic microbes by competing for both nutrition and attachment sites on the lining of the large intestine. The mutualistic bacteria are more at home in the gut than pathogenic bacteria and other microbes, so they are better able to compete for living space. The mutualistic bacteria send chemical signals to the host about the amount of nutrients they need, and the host provides only that much, so harmful bacteria are starved out. The mutualistic gut flora also produce bacteriocins, substances which kill harmful microbes. In soil, microorganisms which live on the root surface of some plants carry out nitrogen fixation. They convert nitrogen gas to nitrogenous compounds that the plants can use. Plants cannot fix nitrogen from the air themselves. Can you tell at a glance which plant in the Figure 1.25 was grown without the help of nitrogen fixing bacteria?

Parasitism

Parasitism is a type of symbiotic relationship between organisms of different species in which one, the parasite, benefits from a long-term, close association, while the other (the host) is harmed. If bacteria form a parasitic associ- ation with other organisms, they are classified as pathogens. There are many examples of bacterial pathogens, which we will discuss later in this lesson. No clear examples of archaeal pathogens are known, although a relationship has been proposed between the presence of some methanogens and human periodontal disease.

Commensalism

Commensalism is a relationship between two living organisms in which one benefits and the other is neither harmed nor helped. Commensal bacteria are found almost everywhere, they grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms on human skin are the cause of body odor.

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FIGURE 1.25 Microbiologist Peter van Berkum com- pares growth of alfalfa plants inoculated with Rhizobium bacteria (left) with plants that haven’t been given the bacteria. Rhi- zobium bacteria live in soil. They fix nitro- gen gas from the air after becoming es- tablished inside root nodules of legumes such as peas, beans, and alfalfa. The rhizobia cannot independently fix nitrogen and require a plant host.

It is estimated that up to 100,000 species of prokaryotes (bacteria and archaea) live in the human body. Most of these organisms are harmless and are called commensal organisms.

Lichens

Lichens, which at first glance look like a crusty or fuzzy piece of dirt on a rock, are actually a symbiotic relationship between a photosynthetic organism and a fungus. The photosynthetic organism is often a cyanobacterium or an alga. Lichens might involve a form of parasitism of the algal or bacterial cells. In laboratory settings, cyanobacteria grow faster when they are alone, rather than when they are part of a lichen. But, the fungus part of the lichen provides the alga or cyanobacterium with water and minerals that the fungus absorbs from whatever the lichen is growing on. The alga or cyanobacteria uses the minerals, water, and sunlight to make food for the fungus and itself. An example of a lichen is shown in the Figure 1.26.

53 1.12. Symbiotic Relationships of Prokaryotes - Advanced www.ck12.org

FIGURE 1.26 Lichens. The lichen Xanthoria parietina is shown here. It has a wide distribution along both the Atlantic and Pacific coasts. It is most commonly found on rocks and walls in coastal areas. Common names for it include common orange lichen, yel- low scale, maritime sunburst lichen, and shore lichen.

Vocabulary

• biological interactions: The interactions between different organisms in an environment.

• commensalism: A symbiotic relationship in which one species benefits while the other species is not affected.

• lichen: A composite organism that results from a mutualistic relationship between a fungus and a cyanobac- terium or green alga.

• mutualism: A type of symbiotic relationship in which both species benefit.

• parasitism: A symbiotic relationship in which one species (the parasite) benefits while the other species (the host) is harmed.

• symbiotic relationship: A close ecological association between two species in which at least one species benefits; this is also known as symbiosis.

Summary

• Usually bacteria live on or in other organisms - their host. These symbiotic relationships can be classified based on whether the host is helped, harmed, or not affected by the microorganisms. Such relationships are respectively classified as mutualistic, parasitic, or commensal.

Practice

Use this resource to answer the questions that follow.

• Prokaryotes and their ecological interactions at https://www.boundless.com/biology/prokaryotes/prokar yotes-and-the-biosphere/prokaryotes-and-their-ecological-interactions/.

54 www.ck12.org Chapter 1. Microbiology - Advanced

Practice Answers

Review

1. Give an example of parasitism, commensalism, and mutualism by prokaryotes. 2. A bacterium lives on its host but does not take any nutrients from the host. It does not harm the host, but it gets shelter from living in the host. What type of relationship exists between these two organisms?

Review Answers

1. Bacterial infections are an example of parasitism. Lichen are an example of commensalism. Nitrogen fixing bacteria are an example of mutualism. 2. This is an example of commensalism.

55 1.13. Human Uses of Prokaryotes - Advanced www.ck12.org

1.13 Human Uses of Prokaryotes - Advanced

• Identify human uses of bacteria. • Identify two industrial and two agricultural uses of bacteria.

What is aromatic black pu-erh tea? Aromatic black pu-erh tea is from the Yunnan Province in China. Leaves undergoes double bacterial and fungal fermentation and are compressed into different forms. Pu-erh tea is used for improving mental alertness and sharp thinking. It is also used for reducing high cholesterol.

Human Uses of Bacteria

Bacteria can be used by humans in a number of useful ways. Despite the fact that some bacteria play harmful roles, such as causing diseases and spoiling food, the industrial and economic importance of bacteria includes both their useful and harmful aspects. Examples of the role of bacteria in industry include the following:

• Fermentation processes, such as brewing, baking, and cheese and butter manufacturing. • Chemical manufacturing, such as the production of ethanol, acetone, organic acids, enzymes, and perfumes. • Pharmaceuticals, such as the manufacture of antibiotics, vaccines, and steroids. • Energy, in the form of biogas (methane). • Food products, such as beverages, dairy products, amino acids, proteins, and nutritional supplements. • Decomposing sewage waste. • Agriculture, such as composting processes and use as pesticides.

Food

Bacteria, often Lactobacillus, along with yeasts and molds, have been used for thousands of years to make fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, beer, and yogurt (some of which are shown in

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the Figure 1.27.) Bacteria are also used in the processing of coffee and cocoa beans but are not found in the end- products (coffee and chocolate). Lactobacillus bacteria also live in the intestines of humans and animals, where their growth inhibits the growth of potentially pathogenic bacteria. These beneficial bacteria are therefore sold as probiotic dietary supplements, such as “live” yogurts.

FIGURE 1.27 Various lactic acid bacteria, including Leuconostoc, Lactobacillus, and Pedio- coccus, are used to pickle vegeta- bles, such as the kimchi dish on the left and sauerkraut (center left, with sausage). Fermented dairy products, such as cheese (center right) and yogurt (right), are made by lactic acid bacteria that digest the milk sugar, lactose. The distinctive flavors of these foods result from the lactic acid that forms when bac- teria ferment the sugars in the vegetables and milk.

Pollution Clean-Up

Some organisms are able to break down compounds such as petroleum or pesticides, which makes them useful in mining, pollution clean-up, and waste processing. Bioremediation is any process that uses microorganisms, fungi, green plants, or their enzymes to clean a contaminant from the environment. Bacteria that can digest the hydrocarbons in petroleum (oil) can be used to clean up oil spills. After the Exxon Valdez oil spill in 1989, fertilizer was added to some of the beaches in Prince William Sound in Alaska, where the accident took place, in order to increase the growth of these naturally occurring bacteria. For more information on the Exxon Valdez oil spill, see the Exxon Valdez Oil Spill Trustee Council web site at http://www.evostc.state.ak.us/facts/index.cfm. Bacteria are also used for the bioremediation of industrial toxic wastes, such as mercury. Certain bacteria can digest organic compounds that are toxic to humans and other animals, such as polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and pesticides.

Microbial Miners

Biomining is the use of prokaryotes to extract certain minerals from ores. Using a bacterium such as Thiobacillus ferooxidans to leach copper from mining leftovers has improved recovery rates and reduced operating costs for mining companies. Also, using microorganisms to leach out the minerals, instead of the traditional methods of high heat or toxic chemicals, is better for the environment.

Waste Disposal and Biogas Production

Aerobic and anaerobic bacteria are used to decompose sewage waste. They break down organic matter into harmless, soluble sludge in settling tanks. The methane gas produced is used as an energy source. The Figure 1.28 shows aerobic digestion of sewage. The wastewater is mixed up, or agitated, which keeps the water oxygenated, allowing aerobic bacteria in the water to break down the waste matter.

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FIGURE 1.28 Pumping air through sewage gives oxy- gen to the bacteria that break down the organic molecules in the waste.

When organic matter is broken down anaerobically, methane gas is produced. Methane gas that is released from landfills and sewage treatment plants can be collected and used as fuel to produce electricity, heat buildings and water, or power vehicles, like the bus in the Figure 1.29. When used as a fuel, methane is often called biogas. Biogas can also be made in special equipment called anaerobic digesters, where waste is broken down in the absence of oxygen. A biogas plant can be fed with crops, such as maize silage, or biodegradable wastes, including sewage sludge and food waste.

FIGURE 1.29 Biogas as fuel for vehicles. The bus is powered by methane gas

Agricultural Uses

Heterotrophic microbes are very common in nature and are responsible for the breakdown of large organic molecules which are generally indigestible to larger animals. They also return nutrients to the soil, such as the nutrients that are locked up in the dead leaves in the Figure 1.30. Prokaryotes and other microorganisms also have important roles in biogeochemical cycles, the cycles that move molecules and nutrients through the biotic and abiotic parts of the environment. Examples include the nitrogen, carbon, and phosphorus cycles. To learn more about biogeochemical

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cycles, see the Recycling Matter concepts in Concept Ecology (Advanced).

FIGURE 1.30 These fallen leaves will be broken down by decomposing bacteria in the soil. De- composition returns the nutrients in the leaves to the soil, where they can be used by other organisms. The aerobic breakdown of biodegradable organic mat- ter, such as leaves, fruits, vegetables, grass clippings, and even animal materi- als, by microorganisms is called compost- ing. The anaerobic breakdown of animal tissues by microorganisms is called putre- faction.

Nutrient Recycling

Bacteria and other microorganisms that are able to digest complex molecules, such as lignin and cellulose, are important in composting. Lignin and cellulose are components of plant cell walls. Composting is the aerobic process of breaking down (decomposing) organic materials into simpler molecules to return nutrients to the soil. Composting is often used in organic gardening and farming. Nitrogen fixing bacteria are also used to increase the nitrogen content of soil. This is done by planting legumes, such as beans or clovers, and allowing the bacteria in their roots to fix nitrogen into the soil for some time. The legumes and their resident bacteria are then tilled into the soil so that other crops can be planted.

Pest Control

Bacteria can also be used in the place of pesticides. Bacillus thuringiensis are Gram-positive, soil-dwelling bacteria that are used to control certain plant pests. B. thuringiensis produces an endotoxin (called Bt toxin) that is toxic to mosquitoes, moths, and certain caterpillars. Because of its limited toxicity to certain insects, Bt toxin is regarded as environmentally friendly. It does not affect humans, wildlife, pollinators, and most other beneficial insects, such as ladybugs and bees. Bt toxin has been genetically engineered into crops (see Concept Biotechnology (Advanced)).

Vocabulary

• biogas: A gas produced by the breakdown of organic matter in the absence of oxygen.

• biomining: The bacterial extraction of certain minerals from ores.

• bioremediation: Any process that uses microorganisms, fungi, green plants, or their enzymes to clean a contaminant from the environment.

• composting: The aerobic breakdown of biodegradable organic matter, such as leaves, fruits, vegetables, grass clippings, and even animal materials, by microorganisms.

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Summary

• Bacteria are used in fermentation processes, such as brewing, baking, and cheese and butter manufacturing. They are also used in agriculture, such as in composting processes and as pesticides. Bacteria play the key role in nitrogen fixation.

Practice

Use this resource to answer the questions that follow.

• Beneficial Prokaryotes at http://cnx.org/content/m44609/latest/?collection=col11448/latest.

Practice Answers

Review

1. Identify two industrial and two agricultural uses of bacteria.

Review Answers

1. Two industrial uses include waste disposal and biogas production. Two agricultural uses include nutrient recycling and pest control.

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1.14 Prokaryotes and Research - Advanced

• Identify a role of bacteria in biotechnology.

Why are bacteria so often used in research? These scientists are studying a plate of bacteria. Why are bacteria so often used in research? Is it because they are easy to manipulate? Is it because they have a small genome? Is it because they reproduce quickly? The answer to all these questions is yes. But these aren’t the only reasons prokaryotes are used in research.

Prokaryotes in Research

Because they can grow quickly (and they are small), prokaryotes are commonly used in molecular biology, genetics, and biochemistry research. By making mutations in prokaryotic DNA and examining the resulting phenotypes, scientists can discover the function of genes, enzymes, and metabolic pathways in prokaryotes. This knowledge can then be applied to more complex organisms like humans. The understanding of prokaryotic metabolisms and genetics allows biotechnologists to bioengineer bacteria that make medicines and other useful compounds. Biotechnology includes the use of organisms such as bacteria, fungi, and algae in the manufacturing and services industries. For additional information, see the Concept Biotechnology (Advanced).

Biotechnology

Genetic engineering is the manipulation of genes. It is also called recombinant DNA technology. In genetic engineering, pieces of DNA (genes) are cloned by introducing the DNA into a host cell or organism. The foreign DNA is incorporated into the host’s genome and is replicated and passed on to daughter cells. Scientists are able to genetically engineer bacteria to make substances that the bacteria would not normally produce. Bacterial cells are transformed and used in the production of commercially important products. Examples include the production of human insulin, used to treat diabetes, and human growth hormone, which is used to treat pituitary dwarfism. In 1982, Humulin, a genetically engineered form of human insulin, was the first medication produced using modern genetic engineering techniques.

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The bacterium Pseudomonas putida has recently been created by genetic engineering. P. putida can break down petroleum products, such as polystyrene, and solvents, such as toluene, which makes it important in pollution clean- up.

Agrobacterium

An Agrobacterium uses horizontal gene transfer to place genes of interest into plants. Agrobacterium tumefaciens is the most commonly studied species in this genus and contains a plasmid that has tumor inducing genes. Agrobac- terium is well known for its ability to transfer DNA between itself and plants, and, for this reason, it has become an important tool for the genetic engineering of plants. The tumor causing genes from the bacterial plasmid are removed and replaced with a gene of interest. The plasmid is then used in plant transformation. Agrobacterium has been used to transfer genes into various plants, including soybeans, cotton, corn, wheat, alfalfa, and sugar beet.

Vocabulary

• agrobacterium: The use of bacteria in the genetic engineering of plants.

• genetic engineering: The manipulation of an organism’s genes, usually involving the insertion of a gene or genes from one organism into another; this creates DNA sequences that would not normally be found in biological organisms.

Summary

• Bacterial cells are transformed and used in the production of commercially important products, such as human insulin, which is used to treat diabetes, and human growth hormone, which is used to treat pituitary dwarfism.

Practice

Use this resource to answer the questions that follow.

• Agrobacterium : The Natural Genetic Engineer 100 Years Later at http://www.apsnet.org/publicatio ns/apsnetfeatures/Pages/Agrobacterium.aspx.

Practice Answers

Review

1. Identify a role of bacteria in biotechnology. 2. Scientists believe that less than one percent of the total prokaryotes on Earth can be grown in the lab. Why do you think there has been such little success with growing these bacteria and prokaryotes?

Review Answers

1. One use of bacteria in biotechnology is to produce insulin. 2. Many of these bacteria are not adapted to the environment in a lab.

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1.15 Bacterial Diseases - Advanced

• Identify two different ways that bacteria can cause disease in the body.

Would this worry you? It should. This is Lyme disease. Lyme disease is caused by the bacterium Borrelia burgdorferi and needs appropriate medical treatment. If you’re treated with the appropriate antibiotics in the early stages of the disease, you’re likely to recover completely. In later stages, response to treatment may be slower, but the majority of people with Lyme disease do recover completely with the appropriate treatment. Left untreated, this can become very serious.

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Prokaryotes and Disease

For centuries people had no idea about the existence of microorganisms. The causes of infectious diseases were often blamed on misfortune, the displeasure of divine beings with humanity, or poisonous vapors from the sick and dead (miasma theory). The action of tiny, unseen organisms in the spread of disease was suspected but could not be proven. Ancient Indian and Persian texts discussed the role of tiny living things causing sickness and the control of such illnesses. In the mid 16th century, Girolamo Fracastoro, an Italian physician, proposed that epidemic diseases are caused by tiny, transferable particles, or "spores," that could transmit infection by direct or indirect contact. Microorganisms were first directly observed by Anton van Leeuwenhoek, in 1676. But the connection between microbes and disease was not scientifically proven for another 200 years. A German physician, Robert Koch, became famous for showing that the disease anthrax was caused by the bacterium Bacillus anthracis. In 1890, he became the first scientist to offer proof that bacteria cause infectious disease. Koch’s discoveries are now known as the Germ Theory of Disease.

Pathogens

As stated earlier, it is estimated that up to 100,000 species of prokaryotes live in the human body (The estimate is a wide range, from 500 to 100,000). Prokaryotic cells are much smaller than human cells, and there are about ten times as many prokaryotic cells as human cells in the body (estimated at 1,000 trillion prokaryotic cells versus 100 trillion human cells). Much of the body’s population of prokaryotes, the body’s “normal flora,” is found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine, and large intestine). The majority of these bacteria live inside the body, in the large intestine. Many of these are harmless, but a few can cause disease. An infectious disease is a disease that is caused by pathogenic microrganism, including bacteria, viruses, fungi, protozoa, and multicellular parasites. A pathogen is an organism that causes disease or illness to its host. Pathogens can infect both unicellular and multicellular organisms from all of the biological kingdoms. There are several ways in which bacterial pathogens can get into a host. In humans, soil contamination of a wound, bacterial contamination of food, and contact with infected bodily fluids are some common modes of infection. The body contains many natural defenses against some common pathogens:

• The skin, which acts as a physical barrier to microorganisms. • The population of commensal (helpful) bacteria that live in the intestines. • The immune system (including white blood cells and antibodies).

If pathogenic bacteria get past these defenses, they can cause infection and disease. An infection is the colonization of a host organism by a pathogen. In an infection, the infecting organism aims to use the host’s resources to feed and replicate themselves. Generally the host is harmed because the pathogen interferes with homeostasis in the host. This imbalance can lead to inflammation, chronic wounds, poor health, and even death. If the body’s homeostatic balance get damaged, by getting a large or deep wound, killing off gut bacteria with antibiotics, or reducing the numbers of white blood cells (such as in an infection with HIV), pathogenic bacteria have a chance to grow and cause harm to the host. Bacteria that infect the body when the body’s defenses are weakened cause infections known as opportunistic infections. Pathogenic bacteria are a major cause of human death and disease; they cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, food-borne illness, leprosy, and tuberculosis. A pathogenic cause for a known medical disease may only be discovered after many years of research. This was the case with the link between Helicobacter pylori, shown in the Figure 1.31, and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fireblight, and wilts in plants, as well as Johne’s disease (diarrheal disease in cattle), mastitis (infection of milk ducts), and anthrax in farm animals.

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FIGURE 1.31 A scanning electron micrograph image of Helicobacter pylori bacteria attached to human stomach cells. H. pylori bacteria are able to withstand the low pH of stom- ach acids because they secrete an en- zyme that neutralizes the acid. Before H. pylori was linked to peptic ulcers, doctors blamed stress and spicy foods for many ulcers.

Transmission of Disease

An infectious disease is also called a contagious diseases (or communicable disease) when it can be passed from one person to another or from one species to another. Transmission of an infectious disease may occur through physical contact with infected individuals, through liquids, food, body fluids, contaminated objects, airborne inhalation, or spread by a vector. A vector is an organism or an object that does not cause disease itself, but which spreads infection by spreading pathogens from one host to another. Some common vectors of disease are shown in the Figure 1.32. The Table 1.2 lists some contagious bacterial diseases and their modes of transmission and treatments.

TABLE 1.2: Contagious Bacterial Diseases

Bacterium Disease Mode of Transmission Treatment Escherichia coli Urinary tract infection, Fecal-oral route, through Antibiotics for about 10 peritonitis, foodborne ill- contaminated food or wa- days to 2 weeks ness ter

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TABLE 1.2: (continued)

Bacterium Disease Mode of Transmission Treatment Mycobacterium tubercu- Tuberculosis Aerosol droplets from a Antibiotics for 6 to 12 losis sneeze, cough, or spit months Campylobacter jejuni" Campylobacteriosis (diar- Fecal-oral route, through Antibiotics are not nor- rhea, cramping) contaminated food or wa- mally used, disease is ter usually self-limiting Salmonella Gasteroenteritis: Fecal-oral route, through Antibiotics are not nor- diarrhea, fever, vomiting, contaminated food or wa- mally used, disease is and abdominal cramps ter usually self-limiting. In- (Numerous disease- travenous fluids if dehy- causing species) dration occurs

Staphylococcus Skin abscesses, can lead Asymptomatic carriers; Prevention: frequent aureus (Methcillin to sepsis and toxic shock can be picked up and hand-washing, alcohol Resistant—MRSA) syndrome infect wounds (e.g. hand sanitizers. Wound turf burns), sharing of care and cleaning, personal hygiene products antibiotic treatment: (razors, towels). vancomycin Streptococcus pyogenes Group A streptococcal in- Asymptomatic carriers; Antibiotics, such as peni- fections: strep throat; infection can occur cillin scarlet fever. All severe when immune system is GAS infections may lead depressed to shock, organ failure, and death. Helicobacter pylori Stomach ulcers Asymptomatic carriers, Antibiotics spread among people in close contact Bacillus anthracis Anthrax B. anthracis may be inoc- Antibiotics such as peni- ulated into a wound, in- cillin haled, or ingested

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FIGURE 1.32 Transmission of diseases may happen in different ways. Respiratory diseases, such as the common cold, are commonly caught by contact with droplets in the air, which are spread by sneezing or cough- ing. Respiratory and gastrointestinal ill- nesses can also be spread through con- tact with surfaces that many people touch, such as drinking fountains or computer keyboards. Gastrointestinal diseases can be spread by flies. Even our beloved pets can be vectors of diseases, as they tend not to be too concerned about what they chew on.

Vocabulary

• contagious disease: An infectious disease which can be passed from one person to another, or from one species to another; they are also known as a communicable disease.

• infection: The colonization of a host organism by a pathogen.

• infectious disease: A disease that is caused by pathogenic microrganisms, including, bacteria, viruses, fungi, protozoa, and multicellular parasites.

• opportunistic infection: An infection caused by bacteria that infect the body when the body’s defenses are weakened.

• pathogen: A disease-causing agent, such as bacteria and viruses.

• vector: A carrier tool used in genetic engineering to transfer DNA into a target cell; A vector is also an organism or an object that does not cause disease itself, but which spreads infection by spreading pathogens from one host to another.

Summary

• Bacteria can cause disease in two ways: by physically growing and invading tissues and cells or by releasing toxins into the body.

Practice

Use this resource to answer the questions that follow.

• Bacterial Diseases of Humans at http://biology.clc.uc.edu/courses/bio106/bact-dis.htm.

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Practice Answers

Review

1. Identify two different ways that bacteria can cause disease in the body.

Review Answers

1. Bacteria can invade cells or release toxins.

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1.16 Prokaryotic Infections - Advanced

• Identify different ways that bacteria can cause disease in the body.

Shouldn’t tuberculosis be controlled? Yes it should. Tuberculosis is caused by the bacterium Mycobacterium tuberculosis. This disease was at a low for a long time but is now a problem again, because of multiple-drug-resistant strains that have evolved due to the overuse of antibiotics. These bacteria live in the lungs and destroy lung tissue.

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Modes of Infection

Bacteria can cause disease in two ways: by physically growing and invading tissues and cells or by releasing toxins into the body. Endotoxins are usually structural components of the bacterial cell wall which are released mainly when bacteria are lysed. Lipopolysaccharides (LPS) are endotoxic molecules that are found in the outer membranes of various Gram-negative bacteria. There are, however, endotoxins other than LPS. Endotoxins are, in large part, responsible for the symptoms of infections by pathogenic Gram-negative bacteria, such as Neisseria meningitidis, the pathogen that causes meningitis. Exotoxins are proteins excreted by many microorganism, including bacteria, fungi, algae, and protozoa. An exotoxin can cause damage to the host by destroying cells or disrupting cellular metabolism. Both Gram-negative and Gram- positive bacteria produce exotoxins. They are highly potent and can cause major damage to the host. Exotoxins may be secreted, or, similar to endotoxins, may be released during cell lysis. Most exotoxins can be destroyed by heating. They may exert their effect locally or produce systemic effects. Well known exotoxins include the botulinum toxin produced by Clostridium botulinum. Botulinum toxin, which causes botulism, blocks nerve function, leading to paralysis of the respiratory muscles and death. Exotoxins can be blocked by antibodies produced by the immune system, but many exotoxins are so toxic that they may be fatal to the host before the immune system has a chance to mount defenses against them. In these cases, it may be necessary to provide antibodies raised in other hosts to fight the toxins and provide immediate protection.

Food-Borne Illness and Bacteria

Pathogenic bacteria can cause diseases by contaminating food. A foodborne illness is any illness that results from eating or drinking food that is contaminated with a chemical or biological toxin or a pathogen. Most cases of foodborne illness are caused by a variety of foodborne pathogenic bacteria and viruses. Foodborne illness is often called food poisoning, even though the physical effects of foodborne illness are not always caused by a toxin. True food poisoning occurs when a person eats food contaminated with a toxin. Botulism is a food intoxication. Bacteria can also cause illness by growing inside the host’s body after the bacteria have been swallowed in food. The bacteria may invade the cells lining the intestines or may produce a toxin inside the body. The most common bacterial foodborne infections are caused by the bacteria Campylobacter, Salmonella, and E. coli O157:H7. All can be transmitted by the fecal-oral route. The bacteria are excreted in feces and may be transmitted through fecally contaminated water, food, or by person to person contact.

Campylobacter

Campylobacter is a bacterial pathogen that causes fever, diarrhea, and abdominal cramps within two to five days after exposure to the organism. The diarrhea may be bloody, and both nausea and vomiting may occur as well. The illness usually lasts one week. Some people who are infected with Campylobacter don’t have any symptoms at all. It is the most commonly identified bacterial cause of diarrheal illness in the world. Campylobacter species live in the intestines of healthy birds, cattle, pigs, cats, and dogs. The bacteria are spread throughout the environment by their hosts’ feces. As a result, Campylobacter are commonly found in soil. Most raw poultry meat has Campylobacter on it. Eating undercooked chicken or food that has been contaminated by raw chicken meat are the most frequent causes of this infection. See the National Center for Zoonotic, Vector-Borne, and Enteric Diseases (Centers for Disease Control and Prevention) web site, at http://www.cdc.gov/nczved/divisions/dfbmd/ , for additional information.

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Salmonella

Salmonella is also a bacterium that is commonly found in the intestines of birds, reptiles, and mammals . It can be spread to humans in many different foods of animal origin that have been contaminated by feces. Salmonellosis usually includes fever, diarrhea, and abdominal cramps within 12 to 72 hours after infection. The symptoms are a result of the bacteria invading the cells of the intestines, as shown in the Figure 1.33. The illness usually lasts four to seven days, and most people recover without treatment. However, in some people diarrhea may be so severe that the patient needs to be hospitalized. In people with poor health or weakened immune systems, the bacteria can invade the bloodstream and cause life-threatening infections. See the National Center for Zoonotic, Vector-Borne, and Enteric Diseases (Centers for Disease Control and Prevention) web site, at http://www.cdc.gov/nczved/divisi ons/dfbmd/ , for additional information.

FIGURE 1.33 Color-enhanced scanning electron micro- graphs of Salmonella typhimurium (red cells on the left) invading cultured human cells. S. typhimurium can lead to a form of human gastroenteritis sometimes called salmonellosis. The characteristic spiral, or corkscrew, shape of C. jejuni cells can be seen in the micrograph on the right. C. jejuni are the most common cause of bacterial food-related illness in the United States.

E. coli

E. coli O157:H7 is one of hundreds of strains of the bacterium Escherichia coli. Although most strains are harmless, this strain produces a powerful toxin that can cause severe illness. E. coli O157:H7 has been found in the intestines of healthy cattle, deer, goats, and sheep. Human illness usually follows consumption of food or water that has been contaminated with very small amounts of cow feces. Drinking unpasteurized milk, swimming in or drinking fecally contaminated water, and eating contaminated vegetables have also been linked to infection by E. coli O157:H7. The symptoms of this infection are often severe and bloody diarrhea and painful abdominal cramps, usually without fever. In about five percent of cases, a severe complication causes intestinal bleeding, anemia, kidney failure, and possibly death.

Contamination of Food

Bacterial contamination of food usually arises from improper handling, improper preparation, or improper food storage. Good hygiene practices before, during, and after food preparation can reduce the chances of getting an illness. Many foodborne illnesses can be avoided by selecting, cooking, storing, and handling food correctly:

• Check that the food you are about to buy is not damaged, bruised, or spoiled. • Wash your hands often with warm water and soap. • Wash your knives, utensils, and the surfaces on which you prepare food with hot, soapy water. • Wash fruits and vegetables before you eat them. • Store raw and cooked food separately.

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• Cook foods to the proper recommended temperatures. • Store leftovers promptly in a refrigerator set at 4oC (40oF).

Thorough cooking of foods and use of hot water kill most of the disease-causing bacteria that can be found in foods. Ingestion of contaminated food and water remains a leading cause of illness and death in the developing world, particularly for children.

Vocabulary

• endotoxin: A structural component of the bacterial cell wall which is released mainly when bacteria are lysed.

• exotoxin: A protein excreted by many microorganisms, including bacteria, fungi, algae, and protozoa; these toxins cause damage to the host by destroying cells or disrupting cellular metabolism.

• foodborne illness: Any illness that results from eating or drinking food that is contaminated with a chemical or biological toxin or a pathogen.

Summary

• Better food safety, improved hygiene practices, and water treatment have reduced the threat of some pathogens. Though many medical advances have been made to safeguard against infection by pathogens through the use of vaccination and antibiotics, pathogens continue to threaten human life. Personal behaviors also have an influence on a person’s chances of catching an infectious disease.

Practice

Use this resource to answer the questions that follow.

• Bacterial Infections at http://www.lef.org/protocols/infections/bacterial_infection_01.htm.

Practice Answers

Review

1. How has the overuse of antibiotics affected the ability to fight bacterial infections?

Review Answers

1. The overuse of antibiotics have created drug-resistant strains of bacteria that are immune to those antibiotics.

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1.17 Preventions and Treatments for Bacterial Diseases - Advanced

• Examine the role of improved hygiene and better medication in the treatment of disease.

What do tuberculosis, diphtheria, tetanus, pertussis, cholera, typhoid, and Streptococcus pneumoniae have in common? They are all bacterial diseases that can be prevented by vaccinations. Make sure to follow your doctor’s recom- mended vaccination schedule. These vaccines could save your life.

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Preventions and Treatments for Bacterial Diseases

From the beginnings of human civilization, it was recognized that polluted water and improper waste disposal spread diseases. Historically, most effective weapons against infectious diseases have not been medication, but better personal hygiene practices, better nutrition, and proper disposal of sewage and other infectious materials. Things that you can do to reduce your chances of getting or spreading an illness include the following:

• Wash your hands properly and frequently with warm, soapy water for at least 20 seconds. Alcohol hand sanitizers can be very effective at killing bacteria on your hands, but only if your hands are not soiled with dirt. The Centers for Disease Control and Prevention (CDC) has stated that “it is well-documented that the most important measure for preventing the spread of pathogens is effective handwashing.” The effectiveness of handwashing can be demonstrated by the growth on the culture dish below. • Avoid sharing personal products such as cosmetic items (make-up), lotions, toothbrushes, earphones, nail clippers, gym clothes, and towels with other people. This is a common way that Staphylococcal skin infections are transmitted ( Figure below). • Do not approach or handle wild animals: they or their ticks and fleas may carry many illnesses. • Avoid tick, flea, and fly bites by wearing long-sleeved shirts, long socks, and long trousers and using insect repellant when walking in grassy or wooded areas. Always double check yourself for bites and ticks afterward. • Avoid high-risk behaviors, such as unprotected sex and drug use. • Avoid the use of antibiotics in certain situations. Viruses are not killed by antibiotics; for example, antibiotics will not cure the common cold. • Get regular medical checkups. • Get the recommended vaccinations for your age group and before travelling abroad to certain countries.

FIGURE 1.34 Wash your hands! Microbial growth on a blood agar plate from samples taken from individuals without any handwash- ing (section A), after washing hands with soap and water (section B), and after disinfecting hands with alcohol sanitizer (section C). Keep in mind that our hands do also contain some beneficial bacte- rial that consume harmful bacteria. You don’t want constant sterile skin condi- tions. There are probably some beneficial bacterial in (B), however, that is not to say that the use of an alcohol sanitizer is harmful.

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Vocabulary

• antibiotic: A substance produced by or derived from certain fungi, bacteria, and other organisms that can destroy or inhibit the growth of other microorganisms; antibiotics are widely used in the prevention and treatment of infectious diseases.

• infectious disease: A disease that is caused by pathogenic microrganism, including, bacteria, viruses, fungi, protozoa, and multicellular parasites.

• vaccination: The administration of antigenic material (a vaccine) to stimulate an individual’s immune system to develop immunity to a pathogen.

Summary

• Though many medical advances have been made to safeguard against infection by pathogens (vaccination and antibiotics), pathogens continue to threaten human life. Personal behaviors have a great influence on a person’s chances of catching an infectious disease.

Practice

Use this resource to answer the questions that follow.

• Conventional Treatments for Bacterial Infections: Antibiotics and Resistant Bacteria at http://www.lef.o rg/protocols/infections/bacterial_infection_05.htm#treatment.

Practice Answers

Review

1. How does washing your hands help you from getting sick? 2. How has the overuse of antibiotics affected the ability to fight bacterial infections?

Review Answers

1. Washing your hands kills bacteria that could make you sick. 2. The overuse of antibiotics have created drug-resistant strains of bacteria that are immune to those antibiotics.

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1.18 Emerging and Reemerging Diseases - Ad- vanced

• Identify different ways that bacteria can cause diseases in the body.

Are antibiotics a good thing? Yes and no. It is true that the proper use of antibiotics is necessary and extremely beneficial. But the misuse or overuse of these drugs results in antibiotic-resistant bacteria, which can be very dangerous. MRSA is methicillin- resistant Staphylococcus aureus, a bacterium responsible for several difficult-to-treat infections in humans.

Emerging and Reemerging Diseases

In most cases, microorganisms live in harmony with their hosts. Because the microbes and their hosts have evolved together, the hosts gradually become resistant to the microorganisms. When a microbe jumps from a long-time animal host to a human being, it may stop being a harmless symbiont and become pathogenic to the new host. Several human activities have led to the emergence and spread of new diseases. When any of these situations occur, a pathogen that had been confined to a remote habitat appears in a new region or a microbe that had infected only animals may begin to cause disease in humans. These human activities include the following:

• Moving into wildlife habitats. The construction of new homes and housing developments in rural areas brings people into contact with both animals that they would not normally encounter and the microbes that they carry.

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• Changes in agriculture. The introduction of new crops attracts both new crop pests and the microbes that they carry to farming communities, exposing people to unfamiliar diseases. • The destruction of habitats. As countries make use of their natural resources, such as forests, they clear areas for settlement or commercial use, and people encounter insects and other animals harboring previously unknown microorganisms. • Modern transport. Ships and other cargo carriers often harbor unintended "passengers" that can spread diseases to faraway destinations. With international jet airplane travel, people infected with a disease can carry it to distant lands or home to their families, even before their first symptoms appear. • Misuse of antibiotics. The intense use of antibiotics in agricultural food production (chicken, pigs, and cattle) has been associated with the emergence of antibiotic-resistant strains of bacteria, including Salmonella, Campylobacter, Escherichia coli, and Enterococcus species, all of which can cause disease in humans. Self- medication with left-over antibiotics and the over-prescription of antibiotics by doctors has contributed to antibiotic resistant bacteria that are reemerging as health threats in the 21st century. Methicillin resistant Staphlococcus aureus ( MRSA) and multi-drug resistant tuberculosis (MDR TB) (discussed below) are now important public health issues in many countries.

Lyme Disease : An Emerging Disease

Lyme disease is an emerging infectious disease that is caused by the Borrelia burgdorferi bacteria. This bacterium normally lives in mice, squirrels, and other small animals. It is passed from these animals to humans through the bites of certain species of ticks. The infected tick is usually a black-legged or deer tick; the tick is the vector that transmits the disease ( Figure 1.35). The vector is an organism that does not cause a disease itself, but which spreads the disease by carrying the pathogen from one host to another. The ticks do not get Lyme disease, they just pass the Borrelia bacteria into people when biting them. Symptoms of Lyme disease include fever, headache, fatigue, and a characteristic skin rash, shown below. If left untreated, infection can spread to joints, the heart, and the nervous system. Recently, the number of reported cases of Lyme disease has been increasing. The main reason for this is the increased contact between people and the remote areas where the animal hosts and ticks are found. Every year more people are moving into newly constructed areas to live or vacation, and they encounter organisms that they would not normally meet.

FIGURE 1.35 Deer ticks (left) are a common vector of Lyme disease. A bite from an infected tick causes a “bull’s-eye” rash to develop in about 70-80% of infected people. The rash is not an immune reaction, rather, it is a result of infection of the bite site by Borrelia bacteria. Lyme disease was identified when a cluster of cases were identified in three towns in southeastern Connecticut in 1975, including the towns Lyme and Old Lyme, giving the disease its name.

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Reemerging Diseases

Reemerging diseases are diseases that have reappeared after a large decline in their incidence levels. Such diseases are returning because the bacteria that cause them have become more pathogenic. The bacteria that cause these diseases may have become resistant to antibiotics or they may make stronger toxins. Clostridium difficile are Gram- positive, anaerobic, spore-forming bacilli that cause severe diarrhea. Strains of C. difficile have become resistant to antibiotics and produce stronger toxins, which makes C. difficile infections more difficult to treat. Increased and sometimes improper use of antimicrobial drugs has led to the development of resistant pathogens. Many diseases that were formerly treatable with drugs have begun to make a comeback. Hospital-acquired in- fections, such as methicillin resistant Staphlococcus aureus (MRSA) (seen in the Figure 1.36) and vancomycin resistant enterococci, along with community acquired multi-drug resistant tuberculosis (MDR TB), are becoming more common.

FIGURE 1.36 Methicillin Resistant Staphylococcus aureus (MRSA). Skin and wound infec- tions caused by MRSA occur most fre- quently in people who are in hospitals and other healthcare facilities. Recently, however, the numbers of MRSA infections in relatively healthy people have been in- creasing.

Antibiotic Resistance

Bacterial infections are usually treated with antibiotics. There are many types of antibiotics; some antibiotics prevent bacteria from making peptidoglycan, while others prevent bacterial ribosomes from making proteins. Some antibiotics are specific for Gram-positive bacteria, and others are specific for Gram-negative bacteria. Broad- spectrum antibiotics are antibiotics that act against both Gram-positive and Gram-negative bacteria. Amoxicillin is a common broad spectrum antibiotic. Antibiotics are used both in treating human diseases and in certain types of farming, in order to promote animal growth. Some of these practices have contributed to the development of antibiotic resistance in bacterial populations. Antibiotic resistance is the ability of a microorganism to withstand the effects of an antibiotic. Antibiotic resistance evolves naturally by natural selection through mutation. When a population of bacteria is exposed to an antibiotic, only the bacteria that are resistant to the effect of the drug survive. These surviving resistant bacteria will reproduce and become the most common cells in the “final” population, as seen in the Figure 1.37. Once such a gene is generated, bacteria can then pass the "resistance gene" by plasmid exchange to other bacteria. Antibiotic resistance genes are commonly found on bacterial plasmids. If a bacterium carries several resistance genes, it is called multiresistant or a superbug. These have the potential to be very dangerous. See Superbug scenario: Antibiotic resistance will be ’catastrophe’ on par with terrorism at http://rt.com/news/health-medicine-s uperbugs-antibiotics-099/ for additional information.

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FIGURE 1.37 A representation of how antibiotic resis- tance evolves by natural selection. The “Before selection” section represents a population of bacteria before exposure to an antibiotic. The middle “After Selec- tion” section shows the population directly after exposure. Only the most resistant cells survived the antibiotic. The final population is entirely made up of highly resistant bacteria that will not be killed by the antibiotic.

Vocabulary

• antibiotic resistance: The ability of a microorganism to withstand the effects of an antibiotic.

• broad-spectrum antibiotics : Antibiotics that act against both Gram-positive and Gram-negative bacteria.

• MRSA: Methicillin-resistant Staphylococcus aureus, an antibiotic-resistant bacterium responsible for several difficult-to-treat infections in humans.

• reemerging diseases: Diseases that have reappeared after a large decline in their incidence levels.

• superbug: An antibiotic-resistant pathogen; a microorganism that has developed resistance to multiple antibi- otics.

Summary

• Bacterial pathogens can cause both minor and devastating human diseases. Usually, these diseases can be treated with antibiotics. • Antibiotic resistance has created potentially harmful superbugs.

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Practice

Use this resource to answer the questions that follow.

• EMERGING AND RE-EMERGING INFECTIOUS DISEASES at http://www.who.int/inf-fs/en/fact097 .html.

Review

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1.19 Control of Bacteria - Advanced

• Examine the roles of improved hygiene and better medication in the treatment of disease. • Outline the role of personal behaviors in avoiding or treating infectious diseases.

Wouldn’t you want these to be sterile? Sterilization removes bacteria and other disease-causing agents from things like surgical instruments. So, yes, of course you would want these instruments to be sterile. What would happen otherwise?

Control of Bacteria

Today, while many medical advances have been made to safeguard against infections by pathogens, through the use of vaccination and antibiotics, pathogens continue to threaten human life. Social advances such as food safety, hygiene, and water treatment have had a great effect on reducing the threat of some pathogens. The most significant actions that reduced the incidence of infectious diseases were better sanitation, improved personal hygiene practices, better sewage treatment, better nutrition, and better living conditions for people. Over- crowded, unhygienic living conditions are excellent breeding grounds for disease.

Bactericide

A bactericide is a substance that kills bacteria and, preferably, nothing else. Bactericides are either disinfectants, antiseptics, or antibiotics. Disinfectants are antimicrobial agents that are applied to non-living objects (surfaces) to destroy microorganisms. Examples of disinfectants include chlorine bleach and hydrogen peroxide. Disinfectants are different from both antibiotics, which destroy microorganisms within the body, and antiseptics, which destroy microorganisms on living tissue, such as skin. However, there are some viruses and bacteria that are not killed by disinfectants. In hospitals, infections can be prevented by antiseptic measures, such as sterilizing the skin before piercing it with the needle of a syringe. Proper care of catheters and tubing that are placed in a person’s body is important to prevent

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infection, especially by S. aureus, as shown in the the Figure 1.38. Surgical and dental instruments are also sterilized to prevent contamination and infection by bacteria. Doctors, nurses, and other health care personnel are reminded to frequently wash their hands because contaminated hands are a major method of transmission for hospital-acquired illnesses, such as MRSA.

FIGURE 1.38 Staphlococcus aureus bacteria found on the inside of a catheter. The sticky- looking substance between the round cocci bacteria is biofilm, which is made of polysaccharides. Biofilm protects the bacteria from disinfectants, which makes these bacteria very likely to cause an infection in a patient.

Sterilization

Sterilization refers to any process that kills or eliminates disease-causing agents from surfaces, equipment, foods, medications, or biological culture media. A widely-used method for heat sterilization is the autoclave. Autoclaves commonly use steam heated to 121oC (250oF), at 103 kPa (15 psi) above atmospheric pressure. Solid surfaces are sterilized when heated at this temperature for at least 15 minutes or to 134oC for a minimum of 3 minutes. Proper autoclave treatment will inactivate all fungi, bacteria, viruses, and also bacterial spores, which can be quite resistant. Ionizing radiation can be used to sterilize objects such as medical instruments and disposables. The high-energy rays cause lethal mutations to occur in bacterial DNA.

Pasteurization

Cooking is way of killing bacteria that are in food. Most bacteria in food are killed by cooking at temperatures above 60oC (140oF). Pasteurization is the process of heating liquids, such as milk and fruit juice, to destroy pathogens. The process was named after its inventor, French scientist Louis Pasteur. Food can also be sterilized by irradiation. Small doses of ionizing radiation may be used to remove bacteria on food or other organic material. It is important to remember that irradiated food is not radioactive and that radiation only removes the bacteria on the food at that time. It does not prevent future contamination.

Vocabulary

• bactericide: A substance that kills bacteria and, preferably, nothing else.

• disinfectant: Antimicrobial agents that are applied to non-living objects (surfaces) to destroy microorganisms.

• pasteurization: The process of heating liquids, such as milk and fruit juice, to destroy pathogens.

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• sterilization: Any process that kills or eliminates disease-causing agents from surfaces, equipment, foods, medications, or biological culture media.

Summary

Practice

Use this resource to answer the questions that follow.

• The Control of Microbial Growth at http://textbookofbacteriology.net/themicrobialworld/control.html.

Review

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1.20 Microbiology of Viruses - Advanced

• Identify reasons why viruses are not considered to be alive.

What is a virus? One thing is for certain: it is not a bacterium. Is it a cell? No. Does it have proteins? Yes. What else does it have? Only DNA or RNA. Is it alive? Not by today’s definition.

Viruses

"It’s life, Jim, but not as we know it." Misattributed to Spock in the original Star Trek series. What is a virus? Is it a living organism? These are excellent questions. Most virologists consider viruses to be non-living, as viruses do not meet all our definitions of life. They are not made up of cells, so they do not have a cell membrane, cytoplasm, ribosomes, or any other organelles. They do not grow, respire, need ATP, or excrete waste, which almost all known forms of life must do. But they do have proteins and genetic material. Viruses do not replicate by themselves, instead, they use a host cell to make more of themselves. But they do evolve, which is a characteristic of living things. They do not belong to one of the three domains of life, nor do they belong to any one of the six kingdoms. So what exactly is a virus? The term virus comes from the Latin word virus, which means toxin or poison. This may give some hints as to what a virus is. One definition of a virus is a sub-microscopic particle that can infect living cells. In fact, the virus

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must infect a living cell in order to survive. An infected cell will produce viral particles instead of its usual cellular products. Viruses are tiny "organisms" (are they organisms if they do not meet the definition of a living thing?) that may lead to mild or severe illnesses in humans, animals, and plants. They also infect bacteria. Human diseases caused by viruses include the common cold and the flu ( Figure below), as well as the much more severe and life-threatening condition, HIV/AIDS. See Flu Attack! How A Virus Invades Your Body at http://www.npr.org/blogs/krulwich/2011/06/01/114075029/flu-a ttack-how-a-virus-invades-your-body for an overview of viruses.

FIGURE 1.39 Viruses are made of protein and genetic material, as shown here with the influenza virus. As the genetic material is depicted inside the virus, outer structures must then be protein.

Vocabulary

• virologist: A scientist who studies viruses and virus-like agents.

• virus: A sub-microscopic particle that can infect living cells; they contain DNA (or RNA) and can evolve, but lack other characteristics of living organisms.

Summary

• Some scientists disagree as to whether viruses are living. Viruses are not made up of cells, nor do they replicate by themselves. Instead, they use a host cell to make more of copies of themselves. But they do evolve, which is a characteristic of living things.

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Practice

Use this resource to answer the questions that follow.

• Introduction to the Viruses at http://www.ucmp.berkeley.edu/alllife/virus.html.

Review

1. Why are viruses not considered to be living things?

Review Answers

1. Viruses are not composed of cells. In addition, they do not respire or produce waste.

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1.21 Virus Characteristics - Advanced

• Describe the characteristics of viruses, including their reproduction and habitats.

What must a virus do to "stay alive?" First, remember that by today’s definition, it is debatable if viruses are actually alive. In order to make more viruses, viruses must invade a host cell. Above is a depiction an alien-looking virus infecting a bacterial cell. A virus that infects bacteria is known as a bacteriophage.

Characteristics of Viruses

A virus is a sub-microscopic particle that can infect living cells. Viruses are much smaller than prokaryotes, ranging in size from about 20–300 nanometers (nm), though some can be larger. Prokaryotes are typically 0.5–5.0 micrometres (µm) in length. As an example, if a virus were about the size of three soccer balls lying side-by-side, then a prokaryote would be about the size of soccer field. Mimivirus, shown in the Figure 1.40, is the largest known virus, with a diameter of 400 nm. Protein filaments measuring 100 nm stick out from the surface of the virus, which increases the diameter of the virus to about 600 nm. This is bigger than a small bacterial cell. The virus appears hexagonal under an electron microscope; the viral shape is icosahedral (having 20 faces or sides). The study of viruses is known as virology and people who study viruses are known as virologists. Viruses cause several serious human diseases, such as AIDS, influenza, and rabies. Therapy is sometimes difficult for viral

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diseases. Antibiotics have no effect on viruses, and only a few antiviral drugs are available for some diseases. One of the best ways to prevent viral diseases is with vaccines, which produce immunity. But vaccines are available for only a few diseases.

FIGURE 1.40 The largest known virus, called mimivirus, is so large that scientists first mistook it for a bacterium. It was first discovered in amoebae in 1992, and was identified as a virus in 2003. Scientists believe that mimivirus may cause certain types of pneumonia in humans. The core contains DNA, with the majority of the DNA in genes, and only 10% DNA of unknown function ("junk" DNA).

Replication

Viruses can replicate only by infecting a host cell. They cannot reproduce on their own. Viruses are not cells; they are a strand of genetic material within a protective protein coat called a capsid (see Viruses: Structure (Advanced)). They infect a wide variety of organisms, including both eukaryotes and prokaryotes. Once inside the cell, they use the cell’s ATP, ribosomes, enzymes, and other cellular structures to replicate. First, the host cell replicates the viral genome, then it transcribes and translates the viral genes, producing the structural components to package the viral genome and create new viruses.

Habitats

Viruses can be found almost anywhere there is life, including within prokaryotes. A phage is a virus that infects prokaryotes. Phages are estimated to be the most widely distributed and diverse entities in the biosphere, even more numerous than prokaryotic organisms. Phages can be found everywhere their hosts are found, such as in soil, in the intestines of animals, or in seawater. Up to 109 virions (a complete virus particle) have been found in a milliliter of seawater, and up to 70 percent of marine bacteria may be infected by phages. They are also found in drinking water and in some foods, including fermented vegetables and meats, where they control the growth of bacteria.

Vocabulary

• phage: A virus that infects prokaryotes, also known as a bacteriophage.

• virologist: A scientist who studies viruses and virus-like agents.

• virology: The study of viruses.

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• virus: A sub-microscopic particle that can infect living cells; viruses contain DNA (or RNA) and can evolve, but lack other characteristics of living organisms.

Summary

Practice

Use this resource to answer the questions that follow.

• Viruses at http://biology.tutorvista.com/cell/viruses.html.

Review

1. Distinguish between a virus and a phage. 2. In general terms, how do viruses replicate? Could this be considered a type of asexual reproduction? 3. What is one way to prevent viral diseases?

Review Answers

1. Phages are viruses that infect prokaryotes. 2. Viruses replicate by infecting a host cell. While no genetic information is exchanged, the use of a host cell makes viral replication different from most forms of asexual reproduction. 3. Vaccines are quite effective at preventing viral infections.

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1.22 Virus Structure - Advanced

• Outline the basic structure of viruses.

Does it really look like this? Some viruses do. It’s not a simple structure, so it must be complex. But really it is just nucleic acid and protein. The nucleic acid is enclosed in what looks like a "head" region, so everything else must be protein.

Virus Structure

A complete virus particle is called a virion.A virion is made up of nucleic acid (DNA or RNA) surrounded by a protective protein shell called a capsid. The capsid is made from the proteins that are encoded by viral genes. The shape of the capsid serves as one basis for the classification of viruses. The capsid of the mimivirus, shown in the Figure 1.41, is icosahedral. Virally coded proteins will self-assemble to form a capsid. Viruses can have a lipid envelope that is made from the host’s cell membrane when they move out of the cell. The viral envelope helps the virus enter host cells. Many viruses (e.g. influenza and many animal viruses) have viral envelopes covering their protein capsids. If a virus has an outer viral envelope, it usually indicates that the virus exits the host cell by budding off (exocytosis).

Helical Viruses

Helical capsids are made up of a single type of protein subunit stacked around a central axis to form a helical structure. The helix may have a hollow center, which makes it look like a hollow tube. This arrangement results in

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FIGURE 1.41 Diagram of a Cytomegalovirus. The capsid encloses the genetic material of the virus. The envelope which surrounds the capsid is typically made from portions of the host’s cell membranes (phospho- lipids and proteins). Not all viruses have a viral envelope. In this figure, glycopro- teins are identified on the coat of the virus as "Glycoprot."

rod-shaped or filamentous virions. These virions can be anything from short and very rigid, to long and very flexible. The well-studied tobacco mosaic virus (TMV), shown in the Figure 1.42, is an example of a helical virus.

FIGURE 1.42 Tobacco mosaic virus, a helical virus. Al- though their diameters may be very small, some helical viruses can be quite long, as shown here. 1. Nucleic acid 2. Viral protein units 3. Capsid. TMV causes tobacco mosaic disease in tobacco, cu- cumber, pepper, and tomato plants.

Icosahedral Viruses

An icosahedral virus contains a capsid of 20 identical (equilateral) triangles. The icosahedral capsid symmetry gives these viruses a spherical appearance at low magnification. But the protein subunits are actually arranged in a regular geometrical pattern, similar to a soccer ball; they are not truly "spherical," as shown in the Figure 1.43. An icosahedral shape is the most efficient way of creating a hardy structure from multiple copies of a single protein. This shape is used because it can be built from a single basic unit of protein which is used over and over again; this

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saves space in the viral genome. The mimivirus, shown in Viruses: Characteristics (Advanced), is an example of an icosahedral virus.

FIGURE 1.43 Adenovirus, an icosahedral virus. An icosahedron is a three-dimensional shape made up of 20 equilateral triangles. Viral structures are built of repeating, identi- cal protein subunits, making the icosahe- dron the easiest shape to assemble using these subunits.

Complex Viruses

Complex viruses possess capsids which are neither purely helical nor purely icosahedral. These capsids may have extra structures such as protein tails or a complex outer wall. Viral protein subunits will self-assemble into a capsid, but the complex viral DNA also codes for proteins which help in building the viral capsid. Many phage viruses are complex-shaped; they have an icosahedral head bound to a helical tail, as shown in the Figure 1.44. The tail may have a base plate with protein tail fibers. Some complex viruses do not have tail fibers.

Enveloped Viruses

Some viruses are able to surround (envelope) themselves in a portion of their host’s cell membrane; these are known as enveloped viruses. The virus can use either the outer membrane of the host cell or an internal membrane, such as the nuclear membrane or the membrane of the endoplasmic reticulum. In this way, the virus gains an outer lipid bilayer known as a viral envelope. This membrane is studded with proteins coded by both the viral genome and the host genome; however, the lipid membrane itself and any carbohydrates present come entirely from the host cell. The influenza virus, HIV, and the varicella zoster virus, shown in the Figure 1.45, are enveloped viruses. The viral envelope can give a virus some advantages over capsid-only viruses. For example, they have better protection from the host’s immune system, enzymes, and certain chemicals. The proteins in the envelope can include glycoproteins which act as receptor molecules. These receptor molecules allow host cells to recognize and bind the virions, which may result in easier uptake of the virion into the host cell. Most enveloped viruses depend on their

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FIGURE 1.44 These “moon lander” shaped complex viruses infect Escherichia coli bacteria.

FIGURE 1.45 Varicella zoster, an enveloped virus which causes chicken pox and shingles.

envelopes to infect cells. However, because the envelope contains lipids, it makes the virus more susceptible to inactivation by environmental agents, such as detergents that disrupt lipids.

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Vocabulary

• capsid: The protective protein coat of a virus.

• complex virus: A virus with a capsid which is neither purely helical nor icosahedral; these viruses may have extra structures such as protein tails or a complex outer wall.

• enveloped virus: A virus with a lipid viral envelope outside the capsid.

• helical capsid: A capsid made of a single type of protein subunit stacked around a central axis, forming a helical structure.

• icosahedral virus: A virus with a capsid of 20 identical, equilateral triangles.

• viral envelope: A lipid layer surrounding the capsid, which made from the host’s cell membrane.

• virion: A complete virus particle.

Summary

• Viruses are composed of genetic material surrounded by a protective protein shell called a capsid. • Viral structures can include helical, icosahedral, complex, and enveloped.

Practice

Use this resource to answer the questions that follow.

• Virus Structure at https://morgridge.org/wp-content/uploads/2014/09/Virus-Structure.pdf.

Review

1. Draw, label, and compare the structures of a prokaryote and a virus. 2. Describe viral structures.

Review answers

1. Viruses are composed of a protein capsid, a lipid envelope, genetic material, and often additional protein components(e.g. tail fiber, base plate, etc).

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1.23 Virus Discovery - Advanced

• Identify how viruses were discovered.

How were viruses first identified? Using filters. What if you had a filter that could trap all things as small as bacteria? Would viruses be trapped, or would they flow through the filter?

Discovery of Viruses

Viral diseases such as rabies, yellow fever, and smallpox have affected humans for many centuries, but the causes of these diseases were unknown for most of this time. Even though people did not know what caused these diseases, they were still able to prevent some of them. In the late 19th century, French microbiologist Charles Chamberland developed a porcelain filter with pores small enough to trap bacteria, but which allowed smaller particles to filter through. In 1883, Dutch botanist Adolf Mayer first described a tobacco plant disease that could be transferred between plants. The disease was thought to be spread by very small bacteria or toxins. Then in 1889, another Dutch scientist, Martinus Beijerinck, showed that a filtered, bacteria-free culture medium still contained the infectious agent. Russian biologist Dimitri Ivanovski published experiments showing that crushed leaf extracts of infected tobacco plants were still infectious, even after passing the leaf extract through filters that trapped bacteria, demonstrating that the tobacco mosaic disease is caused by something smaller than a bacterium. At about the same time, several independent experiments showed that viruses

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were different from bacteria, yet they could cause disease in living organisms. These experiments also showed that viruses are much smaller than bacteria. In 1915, English bacteriologist Frederick Twort discovered bacteriophage, the viruses that attack bacteria. He noticed tiny clear spots within bacterial colonies and hypothesized that something was killing the bacteria. The invention of electron microscopy in the 1930s allowed scientists to see viruses for the first time. In 1935, American biochemist Wendell Stanley first crystallized the tobacco mosaic virus, shown in the Figure 1.46. Tobacco mosaic virus (TMV) is of course, the particle which Adolf Mayer and Dimitri Ivanovski suggested caused disease in tobacco plants.

FIGURE 1.46 An electron microphotograph of tobacco mosaic virus particles, also called TMV. They were the first viruses to be discov- ered.

Vocabulary

• bacteriophage: A virus that infects and replicates within bacteria, also known as a phage.

• tobacco mosaic virus: A single-stranded RNA virus that infects plants, especially tobacco.

Summary

• Tobacco mosaic virus was the first virus identified when scientists discovered infectious particles smaller than bacteria.

Practice

Use this resource to answer the questions that follow.

• Discovery of Viruses at http://www.odec.ca/projects/2004/lija4j0/public_html/history.htm.

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Review

1. How were viruses discovered?

Review Answers

1. Viruses were first discovered by filtering infectious tobacco leaves. The filtrate was still infectious, indicating that the infection was non-bacterial. Eventually, viruses were visualized in the early 1900s using electron microscopes.

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1.24 Virus Classification - Advanced

• List general methods of viral classification.

Viruses are only protein and DNA. So what’s the difference between them? Well, the shape the proteins take. Some form a round covering, others form other shapes. And it’s not always DNA. It could be RNA. Or single-stranded DNA. So, it is both the protein shape and the type of genetic material that are used to classify viruses.

Classification of Viruses

Like the classification systems for cellular organisms, virus classification is the subject of ongoing debate. This is largely due to the nature of viruses, which cannot truly be classified as either living or non-living. Therefore, viruses do not fit neatly into the biological classification system of cellular organisms, as plants and animal do. Virus classification is based mainly on characteristics of the viral particles, including the capsid shape ( Figure 1.47), the type of nucleic acid (DNA or RNA and double-stranded (ds) or single-stranded (ss)) within the capsid, the process of replication, their host organisms, and the type of disease they cause. The Table 1.3 lists characteristics such as capsid shape, presence of an envelope, and the diseases the viruses can cause.

TABLE 1.3: Viruses

Virus Family Virus Envelope Capsid shape Nucleic Acid Disease Adenoviruses Adenovirus Naked Icosahedral dsDNA upper respiratory infections Parvoviruses Parvovirus Naked Icosahedral ssDNA fifth disease, Canine parvovirus 98 www.ck12.org Chapter 1. Microbiology - Advanced

TABLE 1.3: (continued)

Virus Family Virus Envelope Capsid shape Nucleic Acid Disease Herpesviruses Herpes simplex Enveloped Icosahedral dsDNA Herpes, chicken virus, Varicella pox, shingles, zoster virus, Ep- infectious stein Barr virus mononucleosis Hepadnaviruses Hepatitis B Enveloped Icosahedral dsDNA Hepatitis B virus Reoviruses Rotavirus Naked Icosahedral dsRNA gastroenteritis Retroviruses HIV, HTLV-I Enveloped Complex ssRNA HIV/AIDS, leukemia Orthomyxoviruses Influenzaviruses Enveloped Helical ssRNA Influenza (flu) Rhabdoviruses Rabies virus Enveloped Helical ssRNA Rabies Coronaviruses Corona virus Enveloped Complex ssRNA Common cold, Severe acute respiratory syndrome (SARS) Cystoviruses Cystovirus Enveloped Icosahedral dsRNA Infects Pseudomonas bacteria

To learn more, read Some viruses store genetic information in RNA, at http://www.dnaftb.org/25/ , in which David Baltimore and Howard Temin discuss their work on viruses.

FIGURE 1.47 Morphology of common viruses that infect humans.

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Vocabulary

• virus classification: The process of naming viruses and placing them into a taxonomic system.

Summary

Practice

Use this resource to answer the questions that follow.

• Classification of Viruses at http://www.nlv.ch/Virologytutorials/Classification.htm.

Review

1. Describe how viruses are classified. Give three examples.

Review Answers

1. Viruses are classified according to their envelope, capsid shape, and the presence of double-stranded/single- stranded RNA or DNA. Three such examples are Retroviruses, Adenoviruses, and Coronaviruses.

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1.25 Virus Origins - Advanced

• Describe a possible origin of viruses.

Where did viruses come from? Good question. This represents the AIDS virus, HIV, one of the most researched viruses of all time. Why was such a deadly virus so recently discovered, appearing only in the early 1980s? Does this suggest that viruses are continuously evolving or that new viruses will continuously appear in our future? Maybe.

Origins of Viruses

The origins of modern viruses are not entirely clear. It may be that no single mechanism can account for the origin of all viruses. They do not fossilize well, so molecular techniques have been the most useful means of hypothesizing how they originated. Two main hypotheses currently exist:

1. Small viruses with only a few genes may be runaway stretches of nucleic acid that originally came from the genome of a living organism. Their genetic material could have come from transferable genetic elements such as plasmids or transposons, which can leave and enter genomes. 2. Viruses with larger genomes, such as poxviruses, may have once been small cells which parasitized larger host cells. Over time, genes not required by their parasitic lifestyle would have been lost because they were no longer needed; they provided no selective advantage during evolution. The bacteria Rickettsia and Chlamydia are bacterial cells that, like viruses, can only reproduce inside host cells. Their existence gives weight to this hypothesis, as their parasitic lifestyles are likely to have caused the loss of genes that allow them to survive outside a host cell.

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See Where did viruses come from? at http://www.scientificamerican.com/article.cfm?id=experts-where-did-virus es-come-fr for additional information.

Vocabulary

• plasmid: A small, circular piece of DNA that is physically separate from, and can replicate independently of, chromosomal DNA within a cell.

• transposon: A DNA sequence that can change its position (self-transpose) within the genome of a single cell.

Summary

• Viruses may have originated as breakaway pieces of genetic material from host organisms. Also, they could have originated as intracellular parasites that eventually lost most of their genome.

Practice

Use this resource to answer the questions that follow.

• The Origins of Viruses at http://www.nature.com/scitable/topicpage/the-origins-of-viruses-14398218.

Review

Review Answers

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1.26 Virus Replication - Advanced

• Describe viral replication.

If viruses are not living, how do they make more of themselves? How do viruses reproduce or replicate? They need a host. And the host does all the work for the virus.

Replication of Viruses

Viral populations do not grow through cell division, because they are not cells; instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves. Even though a virus sometimes will not kill the host cell, it can still affect the cell’s homeostasis.

Replication of DNA Viruses

A DNA virus is a virus that uses DNA as its genetic material and replicates using a DNA-dependent DNA poly- merase. The nucleic acid is usually double-stranded DNA but may also be single-stranded DNA. The DNA of DNA viruses is transcribed into mRNA by the host cell. The viral mRNA is then translated into viral proteins by the host cell. These viral proteins then assemble to form new viral particles.

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Replication of RNA Viruses

An RNA virus is a virus that uses ribonucleic acid (RNA) as its genetic material. Their nucleic acid is usually single-stranded RNA but may also be double-stranded RNA. Important human pathogenic RNA viruses include the Severe Acute Respiratory Syndrome (SARS) virus, Influenza virus, and Hepatitis C virus. Animal RNA viruses can be placed into different groups depending on their type of replication.

• Some RNA viruses have their genome used directly as if it were messenger RNA (mRNA). The viral RNA is translated directly into new viral proteins by the host cell, after infection by the virus. • Some RNA viruses carry enzymes which allow their RNA genome to act as a template for the host cell to a form viral mRNA. • Retroviruses use DNA intermediates to replicate. Reverse transcriptase, a viral enzyme that comes from the virus itself, converts the viral RNA into a complementary strand of DNA, which is copied to produce a double stranded molecule of viral DNA. This viral DNA is then transcribed and translated by the host cell’s machinery, directing the formation of new virions. Normal transcription involves the synthesis of RNA from DNA; hence, reverse transcription is the reverse of this process. This is an exception to the central dogma of molecular biology.

Reverse-Transcribing Viruses

A reverse-transcribing virus is any virus which replicates using reverse transcription, the formation of DNA from an RNA template. Some reverse-transcribing viruses have genomes made of single-stranded RNA; these viruses use a DNA intermediate to replicate. Others in this group have genomes that have double-stranded DNA; these viruses use an RNA intermediate during genome replication. The retroviruses, as mentioned above, are included in this group, of which HIV is a member (HIV uses single-stranded RNA as its genetic material). Some double-stranded DNA viruses replicate using reverse transcriptase. The hepatitis B virus is one of these viruses.

FIGURE 1.48 Viral replication using reverse transcrip- tion.

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Bacteriophages

Bacteriophages are viruses that infect bacteria. They bind to surface receptor molecules of the bacterial cell and then their genome enters the cell. The protein coat does not enter the bacteria. (See DNA: The Hereditary Material (Advanced)). Within a short amount of time (just a few minutes in some cases), bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins that help assemble new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane. With some phages, just over twenty minutes after the phage infects the bacterium, over three hundred phages can be assembled and released from the host.

Vocabulary

• bacteriophage: A virus that infects and replicates within bacteria, also known as a phage.

• DNA virus: A virus that uses DNA as its genetic material and replicates using a DNA-dependent DNA polymerase.

• retrovirus: An RNA viruses that uses DNA intermediates to replicate.

• reverse-transcribing virus: A virus which replicates using reverse transcription, the formation of DNA from an RNA template.

• reverse transcriptase: An RNA-dependent DNA polymerase; a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA.

• reverse transcription: The process of transcribing single-stranded RNA into single-stranded DNA.

• RNA virus: A virus that uses ribonucleic acid (RNA) as its genetic material.

Summary

• Viruses replicate using the machinery of a host cell. • Viral DNA genomes are used directly by the host cell; RNA viruses may replicate using a DNA intermediate.

Practice

Use this resource to answer the questions that follow.

• Virus Replication at http://virology-online.com/general/Replication.htm.

Review

1. Compare and contrast DNA virus and RNA virus replication. 2. A classmate says that viruses can only infect eukaryotic cells. Do you agree? Explain your answer.

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Review Answers

1. DNA viruses rely on cellular machinery to transcribe themselves into RNA. In contrast, RNA viruses directly translate themselves into proteins, and often carry their own enzymes to facilitate this. Both systems generate vast amounts of viral protein and nucleic acids, and are effective forms of replication. 2. Viruses are not restricted to eukaryotic cells. Many viruses infect prokaryotic cells and are called phages.

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1.27 Lytic Cycle - Advanced

• Compare the lytic and lysogenic cycles of replication.

What is the first step in viral reproduction? Infection of a host cell. To reproduce or replicate, a virus must use the ribosomes, proteins, and building blocks of a host cell.

Viral Lifecycles: Lytic Cycle

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. These cycles should not be seen as separate; they should rather be seen as two parts of viral reproduction. The lytic cycle is typically considered the main method of viral replication since it results in the destruction of the infected cell and the release of new viruses. The lytic lifecycle of a phage is shown in Figure 1.51. The lytic cycle is a three-stage process.

1. Penetration To infect a cell, a virus must first attach to or enter a cell and inject its genetic material into the cell. The host cell is now infected. If the infected cell is in a multicellular organism, the cell can be targeted for destruction by the immune system.

2. Biosynthesis The virus’ nucleic acid remains separate from the hosts DNA and forms a loop of DNA. The virus uses the host cell’s machinery to make large amounts of viral proteins. In the case of DNA viruses, the DNA is transcribed into messenger RNA (mRNA) molecules that are then translated into proteins.

3. Maturation and lysis

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After many copies of viral components are made, they are assembled into complete viruses. The virus then directs the production of an enzyme that breaks down the host’s cell wall and allows fluid to enter. The cell eventually becomes filled with viruses (usually about 100 to 200) and bursts (lyses) - which gives the lytic cycle its name. The new viruses are then free to infect other cells.

FIGURE 1.49 Bacteriophages infecting bacteria go through the lytic (1, 2, 3) and lysogenic (i, ii, iii) cycles. The lytic and lysogenic cycles are explained in the text.

Lytic Cycle Without Lysis

Some viruses escape the host cell without bursting the cell membrane. Instead, they bud off from it by taking a portion of the membrane with them, or they are released by vacuoles. This is still called lysis because, even though the host cell does not burst and die immediately, this process is otherwise characteristic of the lytic cycle. Lytic cycles without lysis include budding and exocytosis. Influenza viruses bud from their host cells, as shown in the Figure below, and Hepatitis B viruses are released from the host cell from vacuoles. The following describes the steps depicted in the Figure above:

• A virion attaches to the host cell membrane by recognizing specific proteins on the cell’s surface. The virus then enters the cytoplasm by endocytosis. • The envelope wall of the virus breaks down and the genetic material of the virus moves into the the nucleus of the host cell. • In the nucleus, viral polymerases transcribe and replicate the viral RNAs. Newly made viral mRNAs move to cytoplasm where they are translated into viral proteins. • Viral envelope proteins are then moved to the cell membrane by the cell’s Golgi apparatus. • Other viral proteins that are made in the cytoplasm move to the nucleus where they bind with newly made viral genomes (RNA or DNA).

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FIGURE 1.50 Lytic Cycles without lysis. Left, Influenza A virus budding from a cell. Right, Hepatitis C viruses are released in vacuoles, a process called exocytosis. Viruses are able to infect certain cells because their capsid proteins are specific for receptors on the cell’s surface. This specificity determines the host range of a virus. This process has evolved to favor those viruses that only infect cells in which they are capable of replication.

• The newly formed nucleocapsids move into the cytoplasm and toward the cell membrane where viral envelope proteins may be inserted. • The newly made viruses are released from the infected cell.

Viral shedding refers to the production of new viruses, with the newly made viruses leaving the cell to infect other host cells. Viral shedding is often carried out by lysis, in which the cell bursts and dies. Once replication has been completed and the host cell is exhausted of all resources, the viruses may leave the cell.

Vocabulary

• budding: A form of asexual reproduction in which a new organism develops from an outgrowth, or bud, on another one; the bud may stay attached or break free from the parent. Some viruses are released from their host cell by budding.

• exocytosis: The cellular process of secreting materials by vesicle fusion.

• lysogenic cycle: A cycle of viral reproduction in which the viral DNA is incorporated into the host genome.

• lytic cycle: A cycle of viral reproduction in which the virus kills the host, releasing newly formed virions.

• viral shedding: The production of new viruses and the release of the newly made viruses to infect other host cells.

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Summary

• In the lytic cycle, the viral genetic material remains separate from the host DNA. It codes for the production of viral proteins which assemble and burst out of the host cell, killing the host.

Practice

Use this resource to answer the questions that follow.

• Lytic Cycle at http://www.fas.harvard.edu/~biotext/animations/lyticcycle.html.

Review

1. What is the lytic cycle? 2. What does the term “lytic cycle without lysis” mean?

Review Answers

1. In the lytic cycle, viruses replicate alongside their host cells. This does not lead to the immediate destruction of the host cell, in contrast to the lysogenic cycle. 2. In the lytic cycle without lysis, viruses bud off viral particles using small sections of membrane.

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1.28 Lysogenic Cycle - Advanced

• Compare the lytic and lysogenic cycles of replication.

What happens when the viral genome fuses with the host genome? That fusion of the genomes is known as lysogeny or the lysogenic cycle. It is part of the viral "life cycle" and results in many new host cells that contain the viral genome.

Lysogenic Cycle

Viruses that infect prokaryotes and eukaryotes can both enter the lysogenic cycle and also the lytic cycle. The lysogenic cycle is shown in the lower portion of the Figure 1.51. When infecting a cell, some DNA phages only lyse a small fraction of the cells they infect. Sometimes the phage DNA is incorporated into the host’s chromosome and replicates along with the host DNA. This occurs as part of the lysogenic cycle. Once the viral DNA is incorporated into the host genome, the viral DNA is called a prophage. During the lysogenic state, the information contained in the viral DNA is not expressed. But the prophage is copied like the rest of the DNA and is passed on to every daughter cell. For example, the Herpes Simplex Virus first enters the lytic cycle after infecting a human. It then enters the lysogenic cycle before travelling to the nervous system where it lies quietly in nerve fibers. After a period of time in the latent stage (perhaps months or years), the herpes virus can reactivate to the lytic stage, during which it may cause disease symptoms similar to those during the initial infection. The lysogenic cycle can be divided into three stages, as shown in the Figure 1.51:

i. Fusion of Genetic Material Lysogeny is characterized by the fusion of the viral nucleic acid with that of the host cell.

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FIGURE 1.51 Bacteriophages infecting bacteria go through the lytic (1, 2, 3) and lysogenic (i, ii, iii) cycles. The lytic and lysogenic cycles are explained in the text.

ii. Replication of the Prophage The newly integrated prophage can be passed on to daughter cells during every cell division. Cells containing the prophage may replicate many times.

iii. Prophage Leaves Host DNA At a later point, the prophage may disassociate from the host DNA. As a result, the virus has entered the lytic cycle and virus particles are made by the host cell. The result of a virus infecting a human cell can be seen in the Figure 1.52.

Vocabulary

• lysogenic cycle: A cycle of viral reproduction in which the viral DNA is incorporated into the host genome.

• prophage: A phage (viral) genome that is either inserted and integrated into the circular bacterial DNA chromosome or exists as an extrachromosomal plasmid.

Summary

• In the lysogenic cycle, the viral DNA gets integrated into the host’s DNA but viral genes are not expressed. The prophage is passed on to daughter cells during every cell division. After some time, the prophage leaves the bacterial DNA and goes through the lytic cycle, creating more viruses.

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FIGURE 1.52 Cold sores are caused by the herpes simplex 1 virus. A person who has her- pes simplex 1 viruses in their body will experience outbreaks of painful blisters on or around their lips. The outbreaks happen when the virus reactivates into the lytic cycle after quietly going through the lysogenic cycle for some time. For further information see the Medline plus web site at http://www.nlm.nih.gov/medli neplus/herpessimplex.html.

Practice

Use this resource to answer the questions that follow.

• Lysogeny at http://sites.fas.harvard.edu/~biotext/animations/lysogeny.html.

Review

1. Compare the lytic and lysogenic life cycles.

Review Answers

1. Both cycles are methods for viruses to replicate themselves. The cycles often alternate, depending on environ- mental conditions. However, they are distinct in that the lysogenic cycle results in the death of the host cell, while the lytic cycle results in a more dormant form of infection.

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1.29 Viral Disease - Advanced

• Identify viral diseases of humans. • Identify the link between viruses and cancer.

How does a virus cause disease? If a cell spends time and energy replicating a viral genome, transcribing and translating viral proteins, and assembling viral particles, is it involved in maintaining homeostasis? What if the host cell is destroyed by lysis? The answers to both of these questions is that the actions of the virus on the host cell disrupts homeostasis.

Viruses and Disease

One main reason to study viruses is the fact that they cause many important infectious diseases, including the common cold, influenza, rabies, measles, many forms of diarrhea, hepatitis, yellow fever, polio, smallpox, and AIDS. Plant viruses can cause losses in food and crop production. Some viruses, known as oncoviruses, can lead to certain forms of cancer. The best studied example of an oncovirus is the association between Human papillomavirus (HPV) and cervical cancer.

Viruses and Human Disease

Examples of common human diseases caused by viruses include the common cold, the flu, chickenpox, and cold sores. Serious diseases, such as Ebola, AIDS, and avian influenza, are also caused by viruses. The specific binding between the viral capsid proteins and specific receptors on the host’s cellular surface determines the host range of a virus. For example, the human immunodeficiency virus (HIV) infects only human T cells because its surface protein interacts with protein receptors on the T cell’s surface.

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As you have already learned, viruses can cause disease in a number of different ways, one of which is by cell lysis. Other viruses can cause disease without killing the host cell. Although viruses can disrupt homeostasis, causing disease, they may also exist relatively harmlessly within an organism. An example of a harmless existence is the life cycle of the herpes simplex virus. This virus causes cold sores, and it can remain in a dormant state within the human body, a period of time called latency. Latency is also a characteristic of the varicella zoster virus which causes chicken pox. Latent chickenpox infections return in later life as the disease called shingles. Shingles is characterized by a painful skin rash with blisters in an area on one side of the body, as shown in the Figure 1.53. It results from the reactivation of the latent varicella zoster virus that lie dormant in nerves.

FIGURE 1.53 Shingles (herpes zoster) outbreak across the neck and face. It is caused by a reac- tivation of the chicken pox virus (Varicella zoster) that has laid hidden in nerve cells since the person had chicken pox. In this man’s case, the viruses emerged from nerve endings in the neck. You cannot “catch” shingles from a person with the shingles rash, but you could catch chick- enpox from them, unless you have been vaccinated against chickenpox.

Some viruses can cause life-long or chronic infections where the viruses continue to replicate in the body despite the hosts’ defense mechanisms. A chronic infection or disease is long-lasting and happens again and again. Hepatitis B viruses and Hepatitis C viruses cause chronic infections. People chronically infected with Hepatitis B virus are known as carriers, who act as reservoirs for infectious viruses, passing them onto other people.

The Flu

Influenza, or the flu, spreads around the world in seasonal epidemics. An epidemic is an outbreak of a disease within a population of people during a specific time. Every year in the United States, about 200,000 people are hospitalized and 36,000 people die from the flu. Flu pandemics can kill millions of people. A pandemic is an epidemic that spreads through human populations across a large region (for example a continent) or even worldwide. Three

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influenza pandemics occurred in the 20th century and killed tens of millions of people. Each of these pandemics was caused by the appearance of a new strain of the virus. Most influenza strains can be inactivated easily by disinfectants and detergents. Influenza (commonly called the flu) is a contagious respiratory illness caused by influenza viruses. Influenza usually starts suddenly and may include the following common symptoms:

• Fever (usually high). • Headache. • Tiredness (can be extreme). • Cough. • Sore throat. • Runny or stuffy nose. • Body aches. • Diarrhea and vomiting (more common among children than adults).

Many people who have a stomach problem refer to it as the "stomach flu," which, medically speaking, does not exist.

HIV

Most researchers believe that the human immunodeficiency virus (HIV) originated in sub-Saharan Africa during the 20th century. HIV is transmitted by sexual contact and by contact with infected bodily fluids, such as blood, semen, breast milk, and vaginal secretions. It is also passed from mother to fetus. HIV is now a pandemic, with an estimated (as of 2008) 38.6 million people now living with the disease worldwide. It is estimated that AIDS has killed more than 25 million people since it was first recognized in 1981. HIV/AIDS is further discussed in The Immune System: HIV and AIDS (Advanced). For further information about HIV/AIDS, see the CDC (Centers for Disease Control and Prevention) web site at http://www.cdc.gov/hiv/resources/factsheets/. HIV is a retrovirus that destroys the human immune system. HIV primarily infects helper T cells (specifically CD4+ T cells), macrophages, and dendritic cells. HIV infection leads to low levels of CD4+ T cells because the virus directly kills infected cells, and the infected T cells are also attacked by the immune system. The infection of a CD4 cell is shown in the Figure 1.54. When CD4+ T cell numbers decline below a certain critical level, cell-mediated immunity is lost, and the body becomes more prone to opportunistic infections. If left untreated, most HIV-infected individuals will develop Acquired Immunodeficiency Syndrome (AIDS). AIDS is a collection of symptoms and infections resulting from the damage to the immune system by HIV. Because the immune systems of people with AIDS are so weak, bacteria and viruses that do not normally cause disease in healthy people can easily cause disease in an AIDS patient. Opportunistic infections associated with AIDS include:

• Pneumocystis pneumonia, a form of pneumonia caused by a fungus. • Tuberculosis (TB), caused by the Mycobacterium tuberculosis bacteria. • Lung infections caused by Mycobacteria other than tuberculosis (MOTT). • Kaposi’s sarcoma, a type of cancer that is caused by Kaposi’s sarcoma-associated herpesvirus (KSHV).

The Figure 1.54 summarizes how HIV infects a CD4 cell.

1. First, the viral particle attaches to the CD4 receptor and other associated receptors on the cell membrane. The viral envelope then fuses with the cell membrane, and the viral capsid moves into the cell. 2. Once the viral capsid enters the cell, reverse transcriptase frees the single-stranded RNA from the viral proteins and copies it into a complementary strand of DNA. This process of reverse transcription is error-prone, and it is during this step that mutations may occur. Such mutations may cause drug resistance. 3. The reverse transcriptase then makes a complementary DNA strand to form a double-stranded viral DNA (vDNA).

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FIGURE 1.54 Lifecycle of HIV. The image at the bottom right is an SEM of HIV budding from a cultured lymphocyte. The many round bumps on the cell’s surface are sites of assembly and budding of virions.

4. The vDNA is then moved into the cell nucleus. The integration of the viral DNA into the host cell’s genome is carried out by another viral enzyme called integrase. This integrated viral DNA may then lie dormant, during the latent stage of the HIV infection. Clinical latency for HIV can vary between two weeks and 20 years. 5. To actively produce viruses, certain cellular transcription factors need to be present. These transcription factors are plentiful in activated T cells. This means that those cells most likely to be killed by HIV are those currently fighting infection. The provirus is transcribed to mRNA which then leads to new viral protein and genome production. 6. Viral particles are assembled inside the cell and then exit the cell by budding. The virus gets its viral envelope from the cell’s plasma membrane. The cycle begins again when the new particles infect another cell.

HIV infections are treated with a cocktail of several anti-retroviral drugs. The anti-retroviral drugs prevent the virus from replicating and destroying more T cells, thus preventing the patients from developing AIDS. Treatment with anti-retroviral drugs can dramatically increase the life expectancy of people with HIV.

Emerging Viral Diseases

Modern modes of transportation allow more people and products to travel around the world at a faster pace. They also open the airways to the transcontinental movement of infectious disease vectors. One example of this occurring

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was when the West Nile Virus was introduced to the United States (scientists believe) by an infected air traveler. With the use of air travel, people are able to go to foreign lands, contract a disease, and not have any symptoms of illness until they get home, possibly exposing others to the disease along the way. Often, new diseases result from the spread of an existing disease from animals to humans. A disease that can be spread from animals to humans is called a zoonosis. When a disease breaks out, scientists called epidemiologists investigate the outbreak, looking for its cause. Epidemiologists are like detectives trying to solve a crime. The information epidemiologists learn is important to understanding the pathogen and to helping prevent future outbreaks of disease. A deadly strain of avian flu virus named H5N1 has posed the greatest risk for a new influenza pandemic since it first killed humans in Asia in the 1990s. The virus is passed from infected birds to humans. Fortunately, the virus has not mutated to a form that spreads easily between people. Several lethal viruses that cause viral hemorrhagic fever have been discovered, two of which are shown in the Figure 1.55. Ebola outbreaks have been limited mainly to remote areas of the world. However, they have gained extensive media attention because of the high mortality rate —23 percent to 90 percent —depending on the strain. The primary hosts of the viruses are thought to be apes in west central Africa, but the virus has also been isolated from bats in the same region.

FIGURE 1.55 The Ebola virus (left) and Marburg virus (right) are viruses that cause hemorrhagic fevers that can cause multiple organ fail- ures and death.

People get exposed to new and rare zoonoses when they move into new areas and encounter wild animals. For ex- ample, severe acute respiratory syndrome (SARS) is a respiratory disease which is caused by the SARS coronavirus. An outbreak in China in 2003 was linked to the handling and consumption of wild civet cats sold as food in a market. In 2005, two studies identified a number of SARS-like coronaviruses in Chinese bats. It is likely that the virus spread from bats to civets and then to humans.

Ebola

Ebola is a rare and deadly disease caused by infection with a strain of Ebola virus. The 2014 Ebola epidemic is the largest in history, affecting multiple countries in West Africa, including Guinea, Sierra Leone and Liberia. Ebola is spread through direct contact with blood and body fluids of a person infected by and already showing symptoms of Ebola. Ebola is not spread through the air, water, food, or mosquitoes. See Ebola virus disease at http://www.who.i nt/mediacentre/factsheets/fs103/en/ for additional information.

Viruses and Cancer

Certain viruses can cause cancers in humans and other species. The main viruses associated with human cancers are human papillomavirus (HPV), hepatitis B, hepatitis C, Epstein-Barr virus, and human T-lymphotropic virus. Hepatitis viruses, including hepatitis B and hepatitis C, can cause a chronic liver infection that leads to cancer. Infection by human T-lymphotropic virus can lead to leukemia. Kaposi’s sarcoma-associated herpesvirus causes Kaposi’s sarcoma (KS), shown in the Figure 1.56. Epstein–Barr virus causes Burkitt’s lymphoma, Hodgkin’s lymphoma, and cancers of the nose and throat.

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Human Herpesvirus Six (HHV6) is being investigated as a possible cause of neurological diseases such as multiple sclerosis and chronic fatigue syndrome.

FIGURE 1.56 Kaposi’s sarcoma (KS) on the skin of an AIDS patient. KS is a type of blood vessel tumor that is caused by a herpes virus. It is mostly associated with AIDS patients, but it can also occur (rarely) in people who are not infected with HIV.

Human Papillomavirus (HPV)

Papillomaviruses are a diverse group of DNA viruses that infect the skin and mucous membranes of humans and some animals. Over 100 different human papillomavirus (HPV) types have been identified. Some HPV types, such as HPV 1 and 2, cause skin warts. All HPVs are transmitted by skin-to-skin contact. About 30 to 40 HPVs can be transmitted through sexual contact and infect the anogenital region. Genital HPV is the most common sexual transmitted infection in the United States. Some sexually transmitted HPVs may cause genital warts. Infections by about 13 other types of sexually transmitted HPVs can lead to precancerous lesions. These human papillomaviruses are linked to cancers of the cervix, skin, anus, and penis.

Vocabulary

• epidemiologist: A person (scientist or health professional) who studies the patterns, causes, and effects of health and disease conditions in defined populations.

• epidemic: An outbreak of a disease within a population of people during a specific time.

• human papillomavirus (HPV): The most common sexually transmitted virus in the United States; HPV can result in multiple health issues.

• latency: A dormant state within the human body in which viruses can remain.

• oncoviruses: Viruses that can lead to certain forms of cancer.

• pandemic: An epidemic of infectious disease that has spread through human populations across a large region, such as a continent or even worldwide.

• zoonosis: A disease that can be spread from animals to humans.

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Summary

• Diseases caused by viruses include the common cold, the flu, measles, chicken pox, Hepatitis A, and HIV/AIDS. • Some viruses can cause cancer. The human papillomavirus has been linked to cervical cancer, a type of herpes virus causes Kaposi’s sarcoma, and Epstein Barr virus is linked to Burkitt’s lymphoma.

Practice

Use this resource to answer the questions that follow.

• Viral Diseases at http://www.healthgrades.com/conditions/viral-diseases.

Review

1. Name four different viruses that can cause diseases in humans, and identify one disease that each causes. 2. What type of cancer is mostly associated with human papillomavirus? Use this graph that shows the incidence of rotavirus infections over time to answer the following questions.

FIGURE 1.57

3. What months of the year are outbreaks of disease at their highest? 4. What month has the lowest incidence of disease? 5. What is the total time period shown in this graph? (Hint: look to the x-axis) The graph below shows the relationship between the number of HIV particles and CD4 lymphocyte counts over the course of an untreated HIV infection. Use the graph to answer the following question:

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6. How does the increase of the number of HIV particles relate to the path of the disease? 7. Outline what happens to the number of viruses and numbers of lymphocytes between three and six weeks after initial infection.

Review Answers

1. Four examples are HIV (causes AIDS), Influenza (causes the flu), Ebola (causes Ebola), HPV (can lead to cervical cancer). 2. HPV is primarily associated with cervical cancer. 3. Rotavirus outbreaks typically occur in the winter (most notably in January). 4. Rotavirus incidence is lowest in summer (notably in July). 5. This graph spans 5 years. Notably, the graph begins in January and includes 4 more Januaries. 6. After the initial infection, HIV levels are highly related to the course of AIDS. The more HIV particles, the further the disease has progressed. 7. The number of viruses dramatically increases, while the number of lymphocytes significantly decreases. This constitutes the primary infection phase.

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1.30 Control of Viruses - Advanced

• Contrast how vaccines and antiviral medications fight viral diseases.

How are viruses controlled? Luckily, your immune system can control the spread of many viruses. Through the use of vaccinations, you can be immunized against many viruses. This allows your body to fight the virus if it ever comes back to haunt you. Can you kill a virus? Is a virus living? If not, then it cannot be killed.

Control of Viruses

The spread of some viruses can be controlled by good hygiene practices, the same way bacteria can be controlled. Other viral diseases, which can spread quickly from person to person, may be also be prevented and treated by medications. Frequent washing of hands and the importance of other personal hygiene practices were discussed in Prokaryotes: Control of Bacteria (Advanced). Here, we will discuss medical treatments of viral diseases.

Prevention and Treatment of Viral Illnesses

People have been able to control the spread of viruses even before they knew viruses existed. In 1717, Mary Montagu, the wife of an English ambassador to the Ottoman Empire, observed local women inoculating their children against smallpox, a contagious viral disease that was often deadly. Inoculation involves introducing a small amount of live virus into a person’s body to allow their body to build up immunity to the virus. This early smallpox inoculation involved putting smallpox crusts into the nostril of a healthy person.

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Vaccines

Because viruses use the machinery of a host cell to reproduce and often remain dormant within the host, it is difficult to get rid of them without killing the host cell. Vaccines were used to prevent viral infections long before the discovery of viruses. A vaccine is a mixture of antigenic material and other immune stimulants that will produce immunity to a certain pathogen or disease. The term "vaccine" comes from Edward Jenner’s use of cowpox (vacca means cow in Latin) to immunize people against smallpox. The material in the vaccine can either be weakened forms of a living pathogen or virus, dead pathogens (or inactivated viruses), purified material such as viral proteins, or genetically engineered pieces of a pathogen. The material in the vaccine will cause the body to mount an immune response, so the person will develop immunity to the disease. Smallpox was the first disease people tried to prevent by purposely inoculating themselves with other types of infections, such as cowpox. Vaccination is an effective way of preventing viral infections. Vaccinations can be given in schools, health clinics ( Figure 1.58,) and even at home. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps, and rubella. Genetically engineered vaccines are produced through recombinant DNA technology; most new vaccines are produced with this technology.

FIGURE 1.58 A young child receives a vaccine.

A world-wide vaccination campaign by the UN World Health Organization lead to the eradication of smallpox in 1979. Smallpox is a contagious disease unique to humans and is caused by two Variola viruses. The eradication of smallpox was possible because humans are the only carriers of the virus. To this day, smallpox is the only human infectious disease to have been completely eradicated from nature. Scientists are hoping to eradicate polio next.

Antiviral Drugs

While people have been able to prevent certain viral diseases by vaccinations for many hundreds of years, the development of antiviral drugs to treat viral diseases is a relatively recent development. Antiviral drugs are medications used specifically for treating the symptoms of viral infections. The first antiviral drug was interferon, a substance (protein) that is naturally produced by certain immune cells when an infection is detected. Interferons facilitate communication between cells of the immune system to trigger a response against the pathogen. Over the past twenty years, the development of antiviral drugs has increased rapidly. This has been driven by the AIDS epidemic. Like antibiotics, specific antivirals are used for specific viruses. They are relatively harmless to the host, and,

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therefore, can be used to treat infections. Most of the antiviral drugs now available are designed to help deal with HIV and herpes viruses. Antiviral drugs are also available for the influenza viruses and the Hepatitis B and C viruses, which can cause liver cancer. Antiviral drugs are often imitation DNA building blocks which viruses incorporate into their genomes during replication. The life-cycle of the virus is then halted because the newly synthesized DNA is inactive. Similarly to antibiotics, anti-virals are subject to drug resistance, as the pathogens evolve to survive exposure to the treatment. HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. Researchers are now working to extend the range of antivirals to other families of pathogens.

Vocabulary

• antiviral drugs: Medications used specifically for treating the symptoms of viral infections.

• inoculation: Introducing a small amount of live virus into a person’s body to allow their body to build up immunity to the virus.

• interferons: Proteins made and released by host cells in response to the presence of pathogens such as viruses, bacteria, parasites, or tumor cells; they allow for communication between cells to trigger the protective defenses of the immune system that eradicate pathogens or tumors.

• vaccine: A mixture of antigenic material and other immune stimulants that will produce immunity to a certain pathogen/disease.

Summary

• Vaccines prevent viral diseases. Antiviral drugs treat the symptoms of viral infections and attack the virus.

Practice

Use this resource to answer the questions that follow.

• What You Should Know About Flu Antiviral Drugs at http://www.cdc.gov/flu/antivirals/whatyoushould. htm.

Review

Use this image of a public health poster to answer the following two questions:

124 www.ck12.org Chapter 1. Microbiology - Advanced

1. What disease is the subject of this poster? 2. What is the poster asking people to do?

Review Answers

1. The subject of this poster is polio. 2. The poster asks people to get polio vaccines.

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1.31 Viruses in Research - Advanced

• Outline the process of viral therapy.

How can viruses help in research? If you think about it, viruses are really good at delivering DNA. So, what would happen if the viral DNA were replaced with useful DNA? And then, what would happen if that useful DNA were incorporated into the host cell genome and were passed down to future generations of cells? These are important questions that need answers.

Viruses in Research

Viruses are extremely important tools in the study of molecular and cellular biology. Since viruses infect cells by moving their genetic material into the host cell’s nucleus, they are helpful in the investigation of the functions of cells. For example, the use of viruses in research has helped our understanding of the basics of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology.

Viruses and Medicine

Geneticists often use viruses as vectors to introduce genes into cells that they are studying. A viral vector is a tool commonly used by molecular biologists to place genetic material into cells. To be a useful viral vector, the virus is modified so that it will not cause disease, and it will infect only certain types of cells. Phages are often used as vectors to genetically modify bacteria.

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In a similar fashion, viral therapy uses viruses to genetically modify diseased cells and tissues. Viral therapy shows promise as a method of gene therapy and in the treatment of cancer. Gene therapy is the insertion of genes into a person’s cells and tissues to treat a disease. In the case of a genetic disease, the defective gene is replaced with a working gene. Although the technology is still new, it has been used with some success. Scientists have focused on gene therapy for diseases caused by single-gene defects, such as cystic fibrosis, hemophilia, muscular dystrophy, and sickle cell anemia. In gene therapy, the correct version of the gene is introduced to human cells by using a viral vector, such as the adenovirus shown in the Figure 1.59. Phages have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and in Eastern Europe. They are seen as a hope against multi drug resistant strains of many bacteria because they can infect and kill these “superbugs.” However, in the case of MRSA, a phage infecting the bacterium produces a toxin that makes the bacterium more virulent and difficult to contain. Viruses that infect cancer cells are being studied for their use in cancer treatments. Oncolytic viruses are viruses that lyse and kill cancer cells. Some researchers are hoping to treat some cancers with these viruses.

FIGURE 1.59 Gene therapy using an Adenovirus vector. A new gene is inserted into an adenovirus vector, which is used to introduce the modified DNA into a human cell. If the treatment is successful, the new gene will get into the nucleus and into the target cell DNA to make a functional protein.

Vocabulary

• phage: A virus that infects prokaryotes, also known as a bacteriophage.

• vector: A carrier tool used in genetic engineering to transfer DNA into a target cell; an organism or an object that does not cause disease itself but which spreads infection by spreading pathogens from one host to another; a carrier that is used to deliver DNA (often non-functional viral DNA) to the correct location during gene therapy.

• viral therapy: The use of viruses to genetically modify diseased cells and tissues.

• viral vector: A virus-based carrier tool used in genetic engineering to transfer DNA into a target cell.

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Summary

• Gene therapy is the insertion of genes into a person’s cells and tissues to treat a disease. A virus that specifically infects the target cell type may be used to carry the new gene into the cell’s nucleus.

Practice

Use this resource to answer the questions that follow.

• Gene Delivery: Tools Of The Trade at http://learn.genetics.utah.edu/content/genetherapy/gttools/.

Review

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1.32 Prions and Viroids - Advanced

• Compare viriods, prions, and viruses.

Can a virus be only protein? No, a virus must have a genome of some type. But a prion is only protein, meaning there is no nucleic acid. How is this even possible? Obviously a prion is not living, though they can be very dangerous.

Prions and Viroids

Some subviral particles can also cause disease. A prion, short for proteinaceous infectious particle, is a type of infectious agent made only of protein. American neurologist and biochemist Stanley B. Prusiner was awarded the Nobel Prize in physiology or medicine in 1997 for his discovery of prions. Prions cause a number of diseases in different animals, including bovine spongiform encephalopathy (BSE) in cattle (shown in the Figure 1.60), scrapie in sheep, Kuru and Creutzfeldt-Jakob disease (CJD) in humans, and chronic wasting disease (CWD) in elk and deer. (Search for CWD at http://gf.state.wy.us/services/education/cwd/index.asp for additional information on CWD.) All known prion diseases affect the structure of either the brain or other nervous tissue, and all are untreatable and fatal.

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FIGURE 1.60 Microscopic plaques or "holes" are char- acteristic of prion-affected nervous tissue, such as in the brain of this cow. The holes cause the tissue to develop a spongy (spongiform) appearance. Such massive cell death in the nervous system affects the ability of the infected animal to stand or move around.

Creutzfeldt-Jakob Disease

CJD is a very rare disease that causes dementia, memory loss, personality changes, hallucinations, and muscle tremors. The CJD prion is dangerous because it causes normal brain proteins to refold into an abnormal shape. The number of misfolded protein molecules eventually gets very large. They interfere with normal cell function, leading to cell death and, eventually, the death of the patient. Usually, there is a very long incubation period for the disease; people do not usually become ill until late adulthood. However, in the last 15 years there have been several cases of adults younger than 30 getting CJD, mostly in Great Britain. This new form of CJD has been called variant CJD or vCJD. Scientists think that the people who contracted vCJD did so by eating the tissues of cattle infected with BSE. There was a large outbreak of BSE (see above) in the United Kingdom in the early 1990s. During this time, scientist believe that many people may have been exposed to BSE infected foodstuffs, such as meat, bones, and nervous tissue.

Viroids

Viroids are plant pathogens that consist of a very short stretch of circular, single-stranded RNA that does not have a protein coat. They are essentially strands of naked RNA. The smallest viroid discovered so far is 220 nucleotides long. In comparison, the genome of the smallest known viruses capable of causing an infection are around 2,000 bases in size. Viroids were discovered and given their name by an American plant pathologist, Theodor O. Diener, in 1971. Viroid RNA does not code for any known protein. They are usually transmitted by seed or pollen. Infected plants can show distorted growth. The first viroid to be identified was the Potato spindle tuber viroid (PSTVd). About 33 species of viroids have been identified.

Controlling Prions

Prions are infectious by the effect they have on normal versions of proteins. Therefore, deactivating prions involves denaturation of their protein structure. Denaturation is a type of chemical change that changes the shape of a molecule. Once denatured, the prion cannot cause abnormal folding of normal proteins. Prions, however, are quite resistant to denaturation by enzymes, heat, radiation, and formaldehyde treatments, but their infectivity can be reduced by such treatments. However, prions can be denatured by exposing them to temperatures of 134 degrees Celsius for 18 minutes in an autoclave. Ozone sterilization is currently being studied as a potential method for prion deactivation.

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Vocabulary

• prion: Short for proteinaceous infectious particle, a type of infectious agent made only of protein.

• viroid: Plant pathogens that consist of a very short stretch of circular, single-stranded RNA that does not have a protein coat.

Summary

• Viroids are plant pathogens that consist of a very short stretch of circular, single-stranded RNA that does not have a protein coat. They are essentially strands of naked RNA. They are much smaller than viruses. • Prions are protein particles that can cause other proteins to form abnormal shapes, which causes disease.

Practice

Use this resource to answer the questions that follow.

• Prions and Viroids at https://www.boundless.com/biology/textbooks/boundless-biology-textbook/viruses-2 1/prions-and-viroids-139/prions-and-viroids-558-11769/.

Review

1. How do viroids and viruses differ? 2. What is a prion?

Review Answers

1. Viriods are much smaller than viruses (200 nucleotides vs. 2000 nucleotides). They also do not code for any proteins, unlike viruses, and therefore lack a protein coat. 2. A prion is a misfolded protein that causes other proteins to become misfolded.

Summary

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1.33 References

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