Types of Microorganisms

Learning Objectives

  • List the organisms studied in microbiology and describe their defining characteristics
  • Give examples of different types of cellular and viral microorganisms and infectious agents
  • Describe the similarities and differences between archaea and bacteria

Most microbes are unicellular and small enough that they require artificial magnification to be seen. However, there are some unicellular microbes that are visible to the naked eye, and some multicellular organisms that are microscopic. An object must measure about 100 micrometers (µm) to be visible without a microscope, but most microorganisms are many times smaller than that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller than bacteria (Figure 1). See Table 1 for units of length used in microbiology.

A bar along the bottom indicates size of various objects. At the far right is a from egg at approximately 1 mm. To the left are a human egg and a pollen grain at approximately 0.1 mm. Next are a standard plant and animal cell which range from 10 – 100 µm. Next is a red blood cell at just under 10 µm. Next are a mitochondrion and bacterial cell at approximately 1 µm. Next is a smallpox virus at approximately 500 nm. Next is a flu virus at approximately 100 nm. Next is a polio virus at approximately 50 nm. Next are proteins which range from 5-10 nm. Next are lipids which range from 2-5 nm. Next is C60 (fullerene molecule) which is approximately 1 nm. Finally, atoms are approximately 0.1 nm. Light microscopes can be used to view items larger than 100 nm (the size of a flu virus). Electron microscopes are useful for materials from 1.5 nm (larger than an atom) to 1 µm (the size of many bacteria).

Figure 1. The relative sizes of various microscopic and nonmicroscopic objects. Note that a typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 µm), which is at least 10 times smaller than a typical plant or animal cell (~10–100 µm). An object must measure about 100 µm to be visible without a microscope.

Table 1. Units of Length Commonly Used in Microbiology
Metric Unit Meaning of Prefix Metric Equivalent
meter (m) 1 m = 100 m
decimeter (dm) 1/10 1 dm = 0.1 m = 10−1 m
centimeter (cm) 1/100 1 cm = 0.01 m = 10−2 m
millimeter (mm) 1/1000 1 mm = 0.001 m = 10−3 m
micrometer (μm) 1/1,000,000 1 μm = 0.000001 m = 10−6 m
nanometer (nm) 1/1,000,000,000 1 nm = 0.000000001 m = 10−9 m

Microorganisms differ from each other not only in size, but also in structure, habitat, metabolism, and many other characteristics. While we typically think of microorganisms as being unicellular, there are also many multicellular organisms that are too small to be seen without a microscope. Some microbes, such as viruses, are even acellular (not composed of cells).

Microorganisms are found in each of the three domains of life: Archaea, Bacteria, and Eukarya. Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as viruses, do not fall within any of the three domains of life. In this section, we will briefly introduce each of the broad groups of microbes. Later chapters will go into greater depth about the diverse species within each group.

How big is a bacterium or a virus compared to other objects? Check out this interactive website to get a feel for the scale of different microorganisms.

Prokaryotic Microorganisms

Bacteria are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are pathogens, causing disease in humans and other animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have cell walls that contain peptidoglycan.

Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio). Figure 2 shows examples of these shapes.

Each shape designation includes a drawing and a micrograph. Coccus is a spherical shape. Bacillus is a rod shape. Vibrio is the shape of a comma. Coccobacillus is an elongated oval. Spirillum is a rigid spiral. Spirochete is a flexible spiral.

Figure 2. Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rod-shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for Disease Control and Prevention)

They have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. Some bacteria are photosynthetic, such as oxygenic cyanobacteria and anoxygenic green sulfur and green nonsulfur bacteria; these bacteria use energy derived from sunlight, and fix carbon dioxide for growth. Other types of bacteria are nonphotosynthetic

Archaea are also unicellular prokaryotic organisms. Archaea and bacteria have different evolutionary histories, as well as significant differences in genetics, metabolic pathways, and the composition of their cell walls and membranes. Unlike most bacteria, archaeal cell walls do not contain peptidoglycan, but their cell walls are often composed of a similar substance called pseudopeptidoglycan. Like bacteria, archaea are found in nearly every habitat on Earth, even extreme environments that are very cold, very hot, very basic, or very acidic (Figure 3). Some archaea live in the human body, but none have been shown to be human pathogens.

A photograph of a pool of water that changes in color from orange on the edges to blue in the center.

Figure 3. Some archaea live in extreme environments, such as the Morning Glory pool, a hot spring in Yellowstone National Park. The color differences in the pool result from the different communities of microbes that are able to thrive at various water temperatures.

Think about It

  • What are the two main types of prokaryotic organisms?
  • Name some of the defining characteristics of each type.

Eukaryotic Microorganisms

Protozoa, algae (collectively term protists) and fungi are the eukaryotes studied in microbiology.  Although more diseases are caused by viruses and bacteria than by microscopic eukaryotes, these eukaryotes are responsible for some diseases of great public health importance. For example, the protozoal disease malaria was responsible for 584,000 deaths worldwide (primarily children in Africa) in 2013, according to the World Health Organization (WHO). The protozoan Giardia causes a diarrheal illness, known as giardiasis, that istransmitted through contaminated water. In the United States, Giardia is the most common human intestinal parasite (Figure 4). There are fewer fungal pathogens, but these are important causes of illness, as well. On the other hand, fungi have been important in producing antimicrobial substances such as penicillin.

a) A micrograph of kite-shaped cells. B) a single triangular cell with multiple flagella.

Figure 4. (a) A scanning electron micrograph shows many Giardia parasites in the trophozoite, or feeding stage, in a gerbil intestine. (b) An individual trophozoite of G. lamblia, visualized here in a scanning electron micrograph. This waterborne protist causes severe diarrhea when ingested. (credit a, b: modification of work by Centers for Disease Control and Prevention)

Characteristics of Protists

The word protist is a historical term that is now used informally to refer to a diverse group of microscopic eukaryotic organisms. It is not considered a formal taxonomic term because the organisms it describes do not have a shared evolutionary origin. Historically, the protists were informally grouped into the “animal-like” protozoans, the “plant-like” algae, and the “fungus-like” protists such as water molds. These three groups of protists differ greatly in terms of their basic characteristics. For example, algae are photosynthetic organisms that can be unicellular or multicellular. Protozoa, on the other hand, are nonphotosynthetic, motile organisms that are always unicellular. Other informal terms may also be used to describe various groups of protists. For example, microorganisms that drift or float in water, moved by currents, are referred to as plankton. Types of plankton include zooplankton, which are motile and nonphotosynthetic, and phytoplankton, which are photosynthetic.

Protozoans inhabit a wide variety of habitats, both aquatic and terrestrial. Many are free-living, while others are parasitic, carrying out a life cycle within a host or hosts and potentially causing illness. There are also beneficial symbionts that provide metabolic services to their hosts. During the feeding and growth part of their life cycle, they are called trophozoites; these feed on small particulate food sources such as bacteria. While some types of protozoa exist exclusively in the trophozoite form, others can develop from trophozoite to a cyst stage when environmental conditions are too harsh for the trophozoite. A cyst is a dormant cellular form with a protective wall, and the process by which a trophozoite becomes a cyst is called encystment. When conditions become more favorable, these cysts are triggered by environmental cues to become active again and multiply forming trophozoites. One protozoan genus capable of encystment is Giardia.

Protozoans have a variety of reproductive mechanisms. Some protozoans reproduce asexually and others reproduce sexually; still others are capable of both sexual and asexual reproduction.

Many protists have whip-like flagella or hair-like cilia made of microtubules that can be used for locomotion (Figure 4). Other protists use cytoplasmic extensions known as pseudopodia (“false feet”) to attach the cell to a surface; they then allow cytoplasm to flow into the extension, thus moving themselves forward.  (Figure 4)

 

a) Paramecium cell with short strands on the outside labeled cilia. An indent in the outer layer is labeled cytostome. A sphere inside the cell at the base of the cytostome is labeled cytoproct. A star shaped structure inside the cell is labeled contractile vacuole. B) Amoeba cell with projections on the outside labeled pseudopods. The outer layer of the cell is labeled ectoplasm and the inner layer is labeled endoplasm. A sphere inside the cell is labeled contractile vacuole. C) Euglena with a single long flagellum on the outside. The outer layer of the cell is labeled etoplasm, the inner layer is labeled endoplasm. A star shaped structure is labeled contractile vacuole.

Figure 4. (a) Paramecium spp. have hair-like appendages called cilia for locomotion. (b) Amoeba spp. use lobe-like pseudopodia to anchor the cell to a solid surface and pull forward. (c) Euglena spp. use a whip-like structure called a flagellum to propel the cell.

Protists

Protists are unicellular eukaryotes that are not plants, animals, or fungi. Algae and protozoa are examples of protists.

A light micrograph with a black background and glowing cells. The cells have many different shapes ranging from circular to stacks of rectangles to almond shaped. A scale bar indicates how much space 100 microns takes up in this figure.

Figure 5. Assorted diatoms, a kind of algae, live in annual sea ice in McMurdo Sound, Antarctica. Diatoms range in size from 2 μm to 200 μm and are visualized here using light microscopy. (credit: modification of work by National Oceanic and Atmospheric Administration)

Algae (singular: alga) are plant-like protists that can be either unicellular or multicellular (Figure 5). Their cells are surrounded by cell walls made of cellulose, a type of carbohydrate. Algae are photosynthetic organisms that extract energy from the sun and release oxygen and carbohydrates into their environment. Because other organisms can use their waste products for energy, algae are important parts of many ecosystems. Many consumer products contain ingredients derived from algae, such as carrageenan a thickening agent found in ice cream, salad dressing, beverages, lipstick, and toothpaste. Another algal product,  agar, is used as a solidying agent for microbial culture medium

Protozoa (singular: protozoan) are protists that make up the backbone of many food webs by providing nutrients for other organisms. Protozoa are very diverse. Some protozoa move with help from hair-like structures called cilia or whip-like structures called flagella. Others extend part of their cell membrane and cytoplasm to propel themselves forward. These cytoplasmic extensions are called pseudopods (“false feet”). Some protozoa are free-living, whereas others are parasitic, only able to survive by extracting nutrients from a host organism. Most protozoa are harmless, but some are pathogens that can cause disease in animals or humans (Figure 4).

Fungi

Fungi (singular: fungus) include unicellular forms, such as yeast and multicellular forms   such as molds and  mushrooms, Whether unicellular or multicellular, fungal cells have a cell wall containing chitin.

A light micrograph with a clear background and blue cells. A long row of cells forms a central strand. Attached to this are clusters of many spherical cells. Each cell is approximately 5 µm in size and contains a nucleus.

Figure 6. Candida albicans is a unicellular fungus, or yeast. It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants. C. albicans has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism (note the nuclei) and is much larger. (credit: modification of work by Centers for Disease Control and Prevention)

Unicellular fungi are known to have beneficial uses and are used to produce cheese, beer, and wine. However, yeasts can also cause food spoilage and diseases, such as vaginal yeast infections and oral thrush (Figure 6).

The multicellular fungi, called molds are found in many different environments, from soil to rotting food to dank bathroom corners (Figure 7) . Molds play a critical role in the decomposition of dead plants and animals. Some molds can cause allergies, and others produce disease-causing metabolites called mycotoxins. The fungus Aspergillus flavus, a contaminant of nuts and stored grains, produces an aflatoxin that is both a toxin and the most potent known natural carcinogen.  .Molds have been used to make pharmaceuticals, including penicillin, which is one of the most commonly prescribed antibiotics produced by the mold Penicillium

A photograph of a box of moldy oranges.

Figure 7. Large colonies of microscopic fungi can often be observed with the naked eye, as seen on the surface of these moldy oranges.

Think about It

  • Name two types of protists and two types of fungi.
  • Name some of the defining characteristics of each type.

Characteristics of Fungi

Fungi have well-defined characteristics that set them apart from other organisms. Most multicellular fungal bodies, commonly called molds, are made up of filaments called hyphae. Hyphae that have walls between the cells are called septate hyphae; hyphae that lack walls and cell membranes between the cells are called nonseptate or coenocytic hyphae), As hyphae continue to grow, they form a tangled network called a mycelium.  (Figure 8).

Molds can have septate hyphae - long strands with cell walls separating the nuclei. Or they can have coenocytic (nonseptate) hyphae - long strands with no cell wall separating the nuclei. Or they can have pseudohyphae which look like chains of cells with small clusters at intervals

Figure 8. Multicellular fungi (molds) form hyphae, which may be septate or nonseptate. Unicellular fungi (yeasts) cells form pseudohyphae from individual yeast cells.

In contrast to molds, yeasts reproduce asexually by budding off a smaller daughter cell; the resulting cells may sometimes stick together as a short chain or pseudohypha (Figure 1). Candida albicans is an example of a common yeast that is associated with various infections in humans, including vaginal yeast infections, oral thrush, and candidiasis of the skin.

Some fungi are dimorphic, having more than one appearance during their life cycle. That is, they are able to exist in both a unicellular and multicellular form, depending on environmental conditions, such as nutrient availability or fluctuations in temperature, growing as a mold, for example, at 25 °C (77 °F), and as yeast cells at 37 °C (98.6 °F). This ability helps dimorphic fungi to survive in diverse environments. Histoplasma capsulatum, the pathogen that causes histoplasmosis, a lung infection, is an example of a dimorphic fungus (Figure 9).

Drawing of bats in an attic. Fungal body is shown in the guano. A micrograph of the fungus shows hyphae (long strands) withc spheres labeled conidia. The life cycle shows a person inhaling spores which then travel to the lungs and divide into a yeast form. They then travel to the lymph and blood.

Figure 9. Histoplasma capsulatum is a dimorphic fungus that grows in soil exposed to bird feces or bat feces (guano) (top left). It can change forms to survive at different temperatures. In the outdoors, it typically grows as a mycelium (as shown in the micrograph, bottom left), but when the spores are inhaled (right), it responds to the high internal temperature of the body (37 °C [98.6 °F]) by turning into a yeast that can multiply in the lungs, causing the chronic lung disease histoplasmosis. (credit: modification of work by Centers for Disease Control and Prevention)

Fungi carry out sexual and asexual reproduction, involving spores. These spores are specialized cells that, depending on the organism, may have unique characteristics for survival, reproduction, and dispersal. .Asexual spores  have been used in the classification of fungi.

 Summary

  • The fungi include diverse saprotrophic eukaryotic organisms with chitin cell walls
  • Fungi can be unicellular or multicellular; some (like yeast) and fungal spores are microscopic, whereas some are large and conspicuous
  • Reproductive types are important in distinguishing fungal groups

Viruses

Viruses are acellular microorganisms, which means they are not composed of cells. Essentially, a virus consists of proteins and genetic material—either DNA or RNA, but never both—that are inert outside of a host organism. However, by incorporating themselves into a host cell, viruses are able to co-opt the host’s cellular mechanisms to multiply and infect other hosts .Viruses can infect all types of cells, from human cells to the cells of other microorganisms. In humans, viruses are responsible for numerous diseases, from the common cold to deadly Ebola (Figure 10). Most viruses will only be able to infect the cells of one or a few species of organism. This is called the host range. However, having a wide host range is not common and viruses will typically only infect specific hosts and only specific cell types within those hosts.

Figure A is a TEM micrograph showing large circles with many small projections protruding outwards from the edge of the circles. A scale bar shows how large 50 nanometers is relative to this micrograph. Figure B is a TEM micrograph showing long red strands forming a knot-like structure.

Figure 10. (a) Members of the Coronavirus family can cause respiratory infections like the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Here they are viewed under a transmission electron microscope (TEM). (b) Ebolavirus, a member of the Filovirus family, as visualized using a TEM. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Thomas W. Geisbert)

Table 2. Characteristics of Viruses
Infectious, acellular pathogens
Obligate intracellular parasites with host and cell-type specificity
DNA or RNA genome (never both)
Genome is surrounded by a protein capsid and, in some cases, a phospholipid membrane studded with viral glycoproteins
Lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce

Viruses can infect every type of host cell, including those of plants, animals, fungi, protists, bacteria, and archaea.

Viruses that infect bacteria are called bacteriophages, or simply phages. The word phage comes from the Greek word for devour.  Once a cell is infected, the effects of the virus can vary depending on the type of virus. Viruses may cause abnormal growth of the cell or cell death, alter the cell’s genome, or cause little noticeable effect in the cell.

Fighting Bacteria with Viruses

The emergence of superbugs, or multidrug resistant bacteria, has become a major challenge for pharmaceutical companies and a serious health-care problem. According to a 2013 report by the US Centers for Disease Control and Prevention (CDC), more than 2 million people are infected with drug-resistant bacteria in the US annually, resulting in at least 23,000 deaths.[1] The continued use and overuse of antibiotics will likely lead to the evolution of even more drug-resistant strains.

One potential solution is the use of phage therapy, a procedure that uses bacteria-killing viruses (bacteriophages) to treat bacterial infections. Phage therapy is not a new idea. The discovery of bacteriophages dates back to the early 20th century, and phage therapy was first used in Europe in 1915 by the English bacteriologist Frederick Twort.[2] However, the subsequent discovery of penicillin and other antibiotics led to the near abandonment of this form of therapy, except in the former Soviet Union and a few countries in Eastern Europe. Interest in phage therapy outside of the countries of the former Soviet Union is only recently re-emerging because of the rise in antibiotic-resistant bacteria.[3]

Phage therapy has some advantages over antibiotics in that phages kill only one specific bacterium, whereas antibiotics kill not only the pathogen but also beneficial bacteria of the normal microbiota. Development of new antibiotics is also expensive for drug companies and for patients, especially for those who live in countries with high poverty rates.

Phages have also been used to prevent food spoilage. In 2006, the US Food and Drug Administration approved the use of a solution containing six bacteriophages that can be sprayed on lunch meats such as bologna, ham, and turkey to kill Listeria monocytogenes, a bacterium responsible for listeriosis, a form of food poisoning. Some consumers have concerns about the use of phages on foods, however, especially given the rising popularity of organic products. Foods that have been treated with phages must declare “bacteriophage preparation” in the list of ingredients or include a label declaring that the meat has been “treated with antimicrobial solution to reduce microorganisms.”[4]

Think about It

  • Why do humans not have to be concerned about the presence of bacteriophages in their food?
  • What are three ways that viruses can be transmitted between hosts?

Viral Structures

In general, virions (viral particles) are small and cannot be observed using a regular light microscope. They are much smaller than prokaryotic and eukaryotic cells; this is an adaptation allowing viruses to infect these larger cells (see Figure 11). The size of a virion can range from 20 nm for small viruses up to 900 nm for typical, large viruses

Figure a is an electron micrograph showing a virus on the surface of a bacterial cell. The virus has a large head region, a thick neck and thin spider-like legs attached to the bacterium. Figure b is a drawing that labels the outside of the head as the capsid with the viral genome inside. The neck as the sheath and the legs as tail fibers.

Figure 11. (a) In this transmission electron micrograph, a bacteriophage (a virus that infects bacteria) is dwarfed by the bacterial cell it infects. (b) An illustration of the bacteriophage in the micrograph. (credit a: modification of work by U.S. Department of Energy, Office of Science, LBL, PBD)

In 1935, after the development of the electron microscope, Wendell Stanley was the first scientist to crystallize the structure of the tobacco mosaic virus and discovered that it is composed of RNA and protein. In 1943, he isolated Influenza B virus, which contributed to the development of an influenza (flu) vaccine. Stanley’s discoveries unlocked the mystery of the nature of viruses that had been puzzling scientists for over 40 years and his contributions to the field of virology led to him being awarded the Nobel Prize in 1946.

As a result of continuing research into the nature of viruses, we now know they consist of a nucleic acid (either RNA or DNA, but never both) surrounded by a protein coat called a capsid (see Figure 4). The interior of the capsid is not filled with cytosol, as in a cell, but instead it contains the bare necessities in terms of genome and enzymes needed to direct the synthesis of new virions. Each capsid is composed of protein subunits called capsomeres made of one or more different types of capsomere proteins that interlock to form the closely packed capsid.

There are two categories of viruses based on general composition. Viruses formed from only a nucleic acid and capsid are called naked viruses or nonenveloped viruses. Viruses formed with a nucleic-acid packed capsid surrounded by a lipid layer are called enveloped viruses (see Figure 12). The viral envelope is a small portion of phospholipid membrane obtained as the virion buds from a host cell. The viral envelope may either be intracellular or cytoplasmic in origin.

Extending outward and away from the capsid on some naked viruses and enveloped viruses are protein structures called spikes. At the tips of these spikes are structures that allow the virus to attach and enter a cell, like the influenza virus hemagglutinin spikes (H) or enzymes like the neuraminidase (N) influenza virus spikes that allow the virus to detach from the cell surface during release of new virions. Influenza viruses are often identified by their H and N spikes. For example, H1N1 influenza viruses were responsible for the pandemics in 1918 and 2009,[5] H2N2 for the pandemic in 1957, and H3N2 for the pandemic in 1968.

Part A shows a micrograph of atadenovirus, which looks like a wispy sphere that has a larger, flatter structure attached to the bottom. To the right of that is an illustration of the atadenovirus that labels capsomeres, capsids, DNA, and spikes made of glycoproteins. Part B shows the enveloped human immunodeficiency virus in black and white. To the right is an illustration that labels the matrix protein, viral envelope, spikes made of glycoproteins, reverse transcriptase, capsids, and RNA.

Figure 12. Click for a larger image. (a) The naked atadenovirus uses spikes made of glycoproteins from its capsid to bind to host cells. (b) The enveloped human immunodeficiency virus uses spikes made of glycoproteins embedded in its envelope to bind to host cells (credit a “micrograph”: modification of work by NIAID; credit b “micrograph”: modification of work by Centers for Disease Control and Prevention)

Viruses vary in the shape of their capsids, which can be either helical, polyhedral, or complex. A helical capsid forms the shape of tobacco mosaic virus (TMV), a naked helical virus, and Ebola virus, an enveloped helical virus. The capsid is cylindrical or rod shaped, with the genome fitting just inside the length of the capsid. Polyhedral capsids form the shapes of poliovirus and rhinovirus, and consist of a nucleic acid surrounded by a polyhedral (many-sided) capsid in the form of an icosahedron. An icosahedral capsid is a three-dimensional, 20-sided structure with 12 vertices. These capsids somewhat resemble a soccer ball. Both helical and polyhedral viruses can have envelopes. Viral shapes seen in certain types of bacteriophages, such as T4 phage, and poxviruses, like vaccinia virus, may have features of both polyhedral and helical viruses so they are described as a complex viral shape (Figure 13). In the bacteriophage complex form, the genome is located within the polyhedral head and the sheath connects the head to the tail fibers and tail pins that help the virus attach to receptors on the host cell’s surface. Poxviruses that have complex shapes are often brick shaped, with intricate surface characteristics not seen in the other categories of capsid.

Figure a is a helical virus which has a long linear structure. The outer proteins are small spheres arranged into a long, hollow tube. Inside the tube is the genetic material. Tobacco mosaic virus is an example of a helical virus. Figure b is an Icosehedral viruses have a polyhedron structure. The example shown is human rhinovirus which has a pentagon structure. Complex viruses have a more complex structure. The example is variola which has an ovoid structure.

Figure 13. Viral capsids can be (a) helical, (b) polyhedral, or (c) have a complex shape. (credit a “micrograph”: modification of work by USDA ARS; credit b “micrograph”: modification of work by U.S. Department of Energy)

Learning Objectives

  • Distinguish between a lytic and lysogenic life cycle

The Life Cycle of Viruses with Prokaryote Hosts

The life cycle of bacteriophages has been a good model for understanding how viruses affect the cells they infect, since similar processes have been observed for eukaryotic viruses, which can cause immediate death of the cell or establish a latent or chronic infection. Virulent phages typically lead to the death of the cell through cell lysis. Temperate phages, on the other hand, can become part of a host chromosome and are replicated with the cell genome until such time as they are induced to make newly assembled viruses, or progeny viruses.

The Lytic Cycle

During the lytic cycle of virulent phage, the bacteriophage takes over the cell, reproduces new phages, and destroys the cell. There are five stages in the bacteriophage lytic cycle (see Figure 14). Attachment is the first stage in the infection process in which the phage interacts with specific bacterial surface receptors (e.g., lipopolysaccharides and OmpC protein on host surfaces). Most phages have a narrow host range and may infect one species of bacteria or one strain within a species. This unique recognition can be exploited for targeted treatment of bacterial infection by phage therapy or for phage typing to identify unique bacterial subspecies or strains. The second stage of infection is entry or penetration. This occurs through contraction of the tail sheath, which acts like a hypodermic needle to inject the viral genome through the cell wall and membrane. The phage head and remaining components remain outside the bacteria.

This figure outlines the stages of the lytic cycle. Step 1 is attachment when the phage attaches to the surface of the host. The bacteriophage is shown sitting on the surface of the bacterial host cell. Step 2 is penetration when the viral DNA enters the host cell. The image shows DNA from within the virus being injected into the host DNA. Step 3 is biosynthesis when the phage DNA replicates and the phage proteins are made. The image shows various pieces of virus being built within the cell. Step 4 is maturation when the new phage particles are assembled. This shows the viral components being put together in the cell. The fifth step is lysis when the cell lyses and the newly made phages are released. This shows the cell bursting and built viruses being released.

Figure 14. A virulent phage shows only the lytic cycle pictured here. In the lytic cycle, the phage replicates and lyses the host cell.

The third stage of infection is biosynthesis of new viral components. After entering the host cell, the virus synthesizes virus-encoded endonucleases to degrade the bacterial chromosome. It then hijacks the host cell to replicate, transcribe, and translate the necessary viral components (capsomeres, sheath, base plates, tail fibers, and viral enzymes) for the assembly of new viruses. Polymerase genes are usually expressed early in the cycle, while capsid and tail proteins are expressed later. During the maturation phase, new virions are created. To liberate free phages, the bacterial cell wall is disrupted by phage proteins such as holin or lysozyme. The final stage is release. Mature viruses burst out of the host cell in a process called lysis and the progeny viruses are liberated into the environment to infect new cells.

The Lysogenic Cycle

In a lysogenic cycle, the phage genome also enters the cell through attachment and penetration. During the lysogenic cycle, instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host. The integrated phage genome is called a prophage. The process in which a bacterium is infected by a temperate phage is called lysogeny. It is typical of temperate phages to be latent or inactive within the cell.

Some bacteria, such as Vibrio cholerae and Clostridium botulinum, are less virulent in the absence of the prophage. The phages infecting these bacteria carry the toxin genes in their genome and enhance the virulence of the host when the toxin genes are expressed. In the case of V. cholera, phage encoded toxin can cause severe diarrhea; in C. botulinum, the toxin can cause paralysis. During lysogeny, the prophage will persist in the host chromosome until induction, which results in the excision of the viral genome from the host chromosome. After induction has occurred the temperate phage can proceed through a lytic cycle and then undergo lysogeny in a newly infected cell (see Figure 15).

The steps of the lytic and lysogenic cycles. First the phage infects a cell; this shows the virus sitting on the outside of a cell and injecting DNA into the cell. In the next step the phage DNA becomes incorporated into the host genome. In the next step, the cell divides and prophage DNA is passed to the daughter cells. The image shows the cell dividing and the viral DNA within the host genome also being passed to the daughter cell. The next step shows the viral DNA jumping out of the host genome. Under stressful conditions, the prophage DNA is excised from the bacterial chromosomes and enters the lytic cycle. Next, the phage DNA replicates and phage proteins are made. This shows viral pieces being made within the cell. The next step is when the new phage particles are assembled. This shows the virus being build. The final step is when the cell lyses and releases the newly made phages.

Figure 15. A temperate bacteriophage has both lytic and lysogenic cycles. In the lysogenic cycle, phage DNA is incorporated into the host genome, forming a prophage, which is passed on to subsequent generations of cells. Environmental stressors such as starvation or exposure to toxic chemicals may cause the prophage to be excised and enter the lytic cycle.

This video illustrates the stages of the lysogenic life cycle of a bacteriophage and the transition to a lytic phase.

Cultivation of Viruses

Viruses can be grown in vivo (within a whole living organism, plant, or animal) or in vitro (outside a living organism in cells in an artificial environment, such as a test tube, cell culture flask, or agar plate). Bacteriophages can be grown in the presence of a dense layer of bacteria (also called a bacterial lawn) grown in a 0.7 % soft agar in a Petri dish or flat (horizontal) flask (see Figure 16). The agar concentration is decreased from the 1.5% usually used in culturing bacteria. The soft 0.7% agar allows the bacteriophages to easily diffuse through the medium. For lytic bacteriophages, lysing of the bacterial hosts can then be readily observed when a clear zone called a plaque is detected (see Figure 16). As the phage kills the bacteria, many plaques are observed among the cloudy bacterial lawn.

Figure a shows bottles laying on their side with red liquid; the bottles have screw-caps. Figure b shows 3 plates covered in bacterial growth (which is a smooth beige lawn). Each plate has small dots that are regions of no growth. Some plates have many of these plaques some have few.

Figure 16. (a) Flasks like this may be used to culture human or animal cells for viral culturing. (b) These plates contain bacteriophage T4 grown on an Escherichia coli lawn. Clear plaques are visible where host bacterial cells have been lysed. Viral titers increase on the plates to the left. (credit a: modification of work by National Institutes of Health; credit b: modification of work by American Society for Microbiology)

Animal viruses require cells within a host animal or tissue-culture cells derived from an animal. Animal virus cultivation is important for 1) identification and diagnosis of pathogenic viruses in clinical specimens, 2) production of vaccines, and 3) basic research studies. In vivo host sources can be a developing embryo in an embryonated bird’s egg (e.g., chicken, turkey) or a whole animal. For example, most of the influenza vaccine manufactured for annual flu vaccination programs is cultured in hens’ eggs.

The embryo or host animal serves as an incubator for viral replication (see Figure 17). Location within the embryo or host animal is important. Many viruses have a tissue tropism, and must therefore be introduced into a specific site for growth. Within an embryo, target sites include the amniotic cavity, the chorioallantoic membrane, or the yolk sac. Viral infection may damage tissue membranes, producing lesions called pox; disrupt embryonic development; or cause the death of the embryo.

Figure a shows a technician injecting a tray of eggs with a syringe. Figure b shows an egg with syringes in various region such as an outer layer (the chorioallantoic membrane), an inner region called the amniotic cavity and another inner region called the yolk sac. The embryo is connected to the yolk sac and is within the amniotic cavity. Outside the chorioallantoic membrane is albumin and around that is the shell.

Figure 17. (a) The cells within chicken eggs are used to culture different types of viruses. (b) Viruses can be replicated in various locations within the egg, including the chorioallantoic membrane, the amniotic cavity, and the yolk sac. (credit a: modification of work by “Chung Hoang”/YouTube)

For in vitro studies, various types of cells can be used to support the growth of viruses. A primary cell culture is freshly prepared from animal organs or tissues.Then, the virus is added to the culture so that it enters the cells and infects them.  the mixture of cells and viruses is collected and the cells are lysed.  Once the cells are lysed the viruses are released and the microbiologist can collect the viruses by filtration or centrifuguation.

Detection of a Virus

Regardless of the method of cultivation, once a virus has been introduced into a whole host organism, embryo, or tissue-culture cell, a sample can be prepared from the infected host, embryo, or cell line for further analysis under a brightfield, electron, or fluorescent microscope. Cytopathic effects (CPEs) are distinct observable cell abnormalities due to viral infection. CPEs can include loss of adherence to the surface of the container, changes in cell shape from flat to round, shrinkage of the nucleus, vacuoles in the cytoplasm, fusion of cytoplasmic membranes and the formation of multinucleated syncytia, inclusion bodies in the nucleus or cytoplasm, and complete cell lysis (see Table 3).

Further pathological changes include viral disruption of the host genome and altering normal cells into transformed cells, which are the types of cells associated with carcinomas and sarcomas. The type or severity of the CPE depends on the type of virus involved. Table 1 lists CPEs for specific viruses.

Table 3. Cytopathic Effects of Specific Viruses[6]
Virus Cytopathic Effect Example
Paramyxovirus Syncytium and faint basophilic cytoplasmic inclusion bodies  Small structures are seen within a cell.
Poxyvirus Pink eosinophilic cytoplasmic inclusion bodies (arrows) and cell swelling Micrograph of small structures
Herpesvirus Cytoplasmic stranding (arrows) and nuclear inclusion bodies (dashed arrow) The arrow indicates cytoplasmic stranding (seen as an elongation of the cytoplasm). The dashed arrow indicates nuclear inclusion bodies (seen as structures within the nucleus).
Adenovirus Cell enlargement, rounding, and distinctive grape-like clusters distinctive grape-like clusters

Viroids and Prions

Research attempts to discover the causative agents of previously uninvestigated diseases have led to the discovery of nonliving disease agents quite different from viruses. These include particles consisting of RNA only or protein only that are able to self-propagate at the expense of a host. To date, these discoveries include viroids and  prions.

Viroids

Photo of potatoes with odd, lumpy growths.

Figure 18. These potatoes have been infected by the potato spindle tuber viroid (PSTV), which is typically spread when infected knives are used to cut healthy potatoes, which are then planted. (credit: Pamela Roberts, University of Florida Institute of Food and Agricultural Sciences, USDA ARS)

In 1971, Theodor Diener, a pathologist working at the Agriculture Research Service, discovered an acellular particle that he named a viroid, meaning “virus-like.” Viroids consist only of a short strand of circular RNA capable of self-replication. The first viroid discovered was found to cause potato tuber spindle disease, which causes slower sprouting and various deformities in potato plants (see Figure 18). Like viruses, potato spindle tuber viroids (PSTVs) take control of the host machinery to replicate their RNA genome. Unlike viruses, viroids do not have a protein coat to protect their genetic information.

Viroids can result in devastating losses of commercially important agricultural food crops grown in fields and orchards. Since the discovery of PSTV, other viroids have been discovered that cause diseases in plants. Tomato planta macho viroid (TPMVd) infects tomato plants, which causes loss of chlorophyll, disfigured and brittle leaves, and very small tomatoes, resulting in loss of productivity in this field crop.

Think about It

  • What is the genome of a viroid made of?

Prions

At one time, scientists believed that any infectious particle must contain DNA or RNA. Then, in 1982, Stanley Prusiner, a medical doctor studying scrapie (a fatal, degenerative disease in sheep) discovered that the disease was caused by proteinaceous infectious particles, or prions. Because proteins are acellular and do not contain DNA or RNA, Prusiner’s findings were originally met with resistance and skepticism; however, his research was eventually validated, and he received the Nobel Prize in Physiology or Medicine in 1997.

A prion is a misfolded rogue form of a normal protein (PrPc) found in the cell. This rogue prion protein (PrPsc), which may be caused by a genetic mutation or occur spontaneously, can be infectious, stimulating other endogenous normal proteins to become misfolded, forming plaques (see Figure 19). Today, prions are known to cause various forms of transmissible spongiform encephalopathy (TSE) in human and animals.

Figure A shows the process of how normal prion protein is converted to disease causing forms. Endogenous PrPc interact with PrpSC. This converts PRPC into PRPSC. The PRPSC accumulate. Figure B is a micrograph that shows holes in brain tissue.

Figure 19. Endogenous normal prion protein (PrPc) is converted into the disease-causing form (PrPsc) when it encounters this variant form of the protein. PrPsc may arise spontaneously in brain tissue, especially if a mutant form of the protein is present, or it may originate from misfolded prions consumed in food that eventually find their way into brain tissue. (credit b: modification of work by USDA)

TSE is a rare degenerative disorder that affects the brain and nervous system. The accumulation of rogue proteins causes the brain tissue to become sponge-like, killing brain cells and forming holes in the tissue, leading to brain damage, loss of motor coordination, and dementia (see Figure 20). Infected individuals are mentally impaired and become unable to move or speak. There is no cure, and the disease progresses rapidly, eventually leading to death within a few months or years.

The CJD brain has larger spaces as seen by more black regions in the image of the whole brain. The micrograph shows holes in the brain tissue.

Figure 20. Creutzfeldt-Jakob disease (CJD) is a fatal disease that causes degeneration of neural tissue. (a) These brain scans compare a normal brain to one with CJD. (b) Compared to a normal brain, the brain tissue of a CJD patient is full of sponge-like lesions, which result from abnormal formations of prion protein. (credit a (right): modification of work by Dr. Laughlin Dawes; credit b (top): modification of work by Suzanne Wakim; credit b (bottom): modification of work by Centers for Disease Control and Prevention)

TSEs in humans include kuru, fatal familial insomnia, and Creutzfeldt-Jakob disease (see Figure 3). TSEs in animals include mad cow disease, scrapie (in sheep and goats), and chronic wasting disease (in elk and deer). TSEs can be transmitted between animals and from animals to humans by eating contaminated meat or animal feed. Transmission between humans can occur through heredity or by contact with contaminated tissue, as might occur during a blood transfusion or organ transplant. There is no evidence for transmission via casual contact with an infected person.

Prions are extremely difficult to destroy because they are resistant to heat, chemicals, and radiation. Even standard sterilization procedures do not ensure the destruction of these particles. Currently, there is no treatment or cure for TSE disease, and contaminated meats or infected animals must be handled according to federal guidelines to prevent transmission.

Think about It

  • Does a prion have a genome?

Key Concepts and Summary

  • Microorganisms are very diverse and are found in all three domains of life: Archaea, Bacteria, and Eukarya.
  • Archaea and bacteria are classified as prokaryotes because they lack a cellular nucleus. Archaea differ from bacteria in evolutionary history, genetics, metabolic pathways, and cell wall and membrane composition.
  • Archaea inhabit nearly every environment on earth, but no archaea have been identified as human pathogens.
  • Eukaryotes studied in microbiology include algae, protozoa, fungi, and helminths.
  • Protists are a diverse group of eukaryotic organisms that may be unicellular or multicellular.
  • Algae are plant-like protists; protozoa are animal-like protists
  • Microscopic fungi include molds and yeasts.
  • Viruses are acellular microorganisms that require a host to reproduce.

Multiple Choice

Which of the following types of microorganisms is photosynthetic?

  1. yeast
  2. virus
  3. helminth
  4. algae

Which of the following is a prokaryotic microorganism?

  1. helminth
  2. protozoan
  3. cyanobacterium
  4. mold

Which of the following is acellular?

  1. virus
  2. bacterium
  3. fungus
  4. protozoan

Which of the following is a type of fungal microorganism?

  1. bacterium
  2. protozoan
  3. alga
  4. yeast

Which of the following is not a subfield of microbiology?

  1. bacteriology
  2. botany
  3. clinical microbiology
  4. virology

Fill in the Blank

A ________ is a disease-causing microorganism.

Multicellular parasitic worms studied by microbiologists are called ___________.

The study of viruses is ___________.

The cells of prokaryotic organisms lack a _______.

Think about It

  1. Describe the differences between bacteria and archaea.
  2. Name three structures that various protozoa use for locomotion.
  3. Describe the actual and relative sizes of a virus, a bacterium, and a plant or animal cell.
  4. Contrast the behavior of a virus outside versus inside a cell.
  5. Where would a virus, bacterium, animal cell, and a prion belong on this chart?

A bar along the bottom indicates size of various objects. At the far right is a from egg at approximately 1 mm. To the left are a human egg and a pollen grain at approximately 0.1 mm. Next is a red blood cell at just under 10 µm. Next is a mitochondrion at approximately 1 µm. Next are proteins which range from 5-10 nm. Next are lipids which range from 2-5 nm. Next is C60 (fullerene molecule) which is approximately 1 nm. Finally, atoms are approximately 0.1 nm.


  1. US Department of Health and Human Services, Centers for Disease Control and Prevention. "Antibiotic Resistance Threats in the United States, 2013." http://www.cdc.gov/drugresistance/pdf/ar-threats-2013-508.pdf (accessed September 22, 2015).
  2. M. Clokie et al. "Phages in Nature." Bacteriophage 1, no. 1 (2011): 31–45.
  3. A. Sulakvelidze et al. "Bacteriophage Therapy." Antimicrobial Agents and Chemotherapy 45, no. 3 (2001): 649–659.
  4. US Food and Drug Administration. "FDA Approval of Listeria-specific Bacteriophage Preparation on Ready-to-Eat (RTE) Meat and Poultry Products." http://www.fda.gov/food/ingredientspackaginglabeling/ucm083572.htm (accessed September 22, 2015).
  5. J. Cohen. "What’s Old Is New: 1918 Virus Matches 2009 H1N1 Strain. Science 327, no. 5973 (2010): 1563–1564.
  6. Image credits: "micrographs": modification of work by American Society for Microbiology