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Chapter 27. Prokaryotes. Overview: They’re (Almost) Everywhere!. Most prokaryotes are microscopic, but what they lack in size they make up for in numbers There are more in a handful of fertile soil than the number of people who ever lived

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chapter 27

Chapter 27


overview they re almost everywhere
Overview: They’re (Almost) Everywhere!
  • Most prokaryotes are microscopic, but what they lack in size they make up for in numbers
  • There are more in a handful of fertile soil than the number of people who ever lived
  • Prokaryotes thrive almost everywhere, including places too acidic, too salty, too cold, or too hot for most other organisms
  • They have an astonishing genetic diversity

Their collective biological mass (biomass) is at least ten times that of all eukaryotes.

  • What has enabled these tiny organisms to dominate the biosphere throughout their history?
  • One reason for their success is a wealth of adaptations that enable various prokaryotes to inhabit diverse environments. Prokaryotes thrive almost everywhere, including places too acidic, too salty, too cold, or too hot for most other organisms (Figure 27.1) .

Figure 27.1 Orange and yellow colonies of “heat–loving” prokaryotes in the hot water of a Nevada geyser.


They have even been discovered in rocks 2 miles below Earth′s surface.

  • In reconstructing the evolutionary history underlying the varied lifestyles of prokaryotes, biologists are discovering that these organisms have an astonishing genetic diversity.
  • For example, comparing ribosomal RNA reveals that two strains of the bacterial species Escherichia coli are genetically more different than a human and a platypus.
in this chapter
In this chapter…
  • Prokaryotes are classified into two domains, Bacteria and Archaea, which differ in many structural, physiological, and biochemical characteristics.
  • In this chapter, you will read about the remarkable adaptations of prokaryotes, as well as some of the essential ecological services they perform, such as the recycling of chemicals.
  • You will also read about the minority of prokaryotic species that cause serious illness in humans.
  • Finally, you will learn how humans depend on benign prokaryotes for our very survival, and how biotechnology is beginning to harness the metabolic powers of these pervasive organisms
concept 27 1 structural functional and genetic adaptations contribute to prokaryotic success
Concept 27.1: Structural, functional, and genetic adaptations contribute to prokaryotic success
  • Most prokaryotes are unicellular, although some species form colonies
  • Prokaryotic cells have a variety of shapes
  • The three most common of which are spheres (cocci), rods (bacilli), and spirals

Video: Tubeworms


Structural, functional, and genetic adaptations contribute to prokaryotic successMost prokaryotes are unicellular, although some species aggregate transiently or permanently in colonies.

  • Prokaryotic cells typically have diameters in the range of 1–5 μm, much smaller than the 10–100 μm diameter of many eukaryotic cells. (One notable exception is the giant prokaryote Thiomargarita namibiensis, which is about 750 μm in diameter—just visible to the unaided eye

Prokaryotic cells have a variety of shapes, the three most common of which are spheres (cocci), rods (bacilli), and spirals (Figure 27.2) .

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Cocci (singular, coccus ) are spherical prokaryotes. They occur singly, in pairs (diplococci), in chains of many cells (streptococci, shown here), and in clusters resembling bunches of grapes (staphylococci).

  • (b) Bacilli (singular, bacillus ) are rod–shaped prokaryotes. They are usually solitary, but in some forms the rods are arranged in chains (streptobacilli).
  • (c) Spiral prokaryotes include spirilla, which range from comma–like shapes to long coils, and spirochetes (shown here), which are corkscrew–shaped (colorized SEMs).
cell surface structures
Cell-Surface Structures
  • An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment
  • Using the Gram stain, scientists classify many bacterial species into groups based on cell wall composition, Gram-positive and Gram-negative
cell surface structures1
Cell–Surface Structures
  • One of the most important features of nearly all prokaryotic cells is their cell wall, which maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment (see Chapter 7).
  • In a hypertonic environment, most prokaryotes lose water and shrink away from their wall (plasmolyze), like other walled cells. Severe water loss inhibits the reproduction of prokaryotes, which explains why salt can be used to preserve certain foods, such as pork and fish.

The cell walls of prokaryotes differ in molecular composition and construction from those of eukaryotes.

  • As you read in Chapter 5, eukaryotic cell walls are usually made of cellulose or chitin.
  • In contrast, most bacterial cell walls contain peptidoglycan, a network of modified–sugar polymers cross–linked by short polypeptides.
  • This molecular fabric encloses the entire bacterium and anchors other molecules that extend from its surface.
gram staining
Gram staining
  • Using a technique called the Gram stain, developed by Hans Christian Gram, scientists can classify many bacterial species into two groups based on differences in cell wall composition.
  • Gram–positivebacteria have simpler walls with a relatively large amount of peptidoglycan (Figure 27.3a)
  • Gram–negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids) (Figure 27.3b) .

(Click image to enlarge) Figure 27.3 Gram staining. Bacteria are stained with a violet dye and iodine, rinsed in alcohol, and then stained with a red dye. The structure of the cell wall determines the staining response (LM).

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Plasma membrane

Plasma membrane









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Gram staining is a particularly valuable identification tool in medicine.

  • Among pathogenic, or disease–causing, bacteria, gram–negative species are generally more threatening than gram–positive species.
  • The lipopolysaccharides on the walls of gram–negative bacteria are often toxic, and the outer membrane helps protect these bacteria against the body′s defenses.
  • Furthermore, gram–negative bacteria are commonly more resistant than gram–positive species to antibiotics because the outer membrane impedes entry of the drugs.

The effectiveness of certain antibiotics, including penicillin, derives from their inhibition of the peptidoglycan cross–linking, thus preventing the formation of a functional cell wall, particularly in gram–positive bacteria.

  • Such drugs destroy many species of pathogenic bacteria without adversely affecting human cells, which do not contain peptidoglycan.
The cell wall of many prokaryotes is covered by a capsule, a sticky layer of polysaccharide or protein (Figure 27.4).
  • The capsule enables prokaryotes to adhere to their substrate or to other individuals in a colony.
  • Capsules can also shield pathogenic prokaryotes from attacks by their host′s immune system.Figure 27.4 Capsule.
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figure legend
Figure legend
  • The polysaccharide capsule surrounding this Streptococcus bacterium enables the pathogenic prokaryote to attach to cells that line the human respiratory tract—in this image, a tonsil cell (colorized TEM).
Some prokaryotes have fimbriae and pili, which allow them to stick to their substrate or other individuals in a colony
  • Some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae (singular, fimbria ) and pili (singular, pilus ).
  • Fimbriae are usually more numerous and shorter than pili (Figure 27.5)(Click image to enlarge) Figure 27.5 Fimbriae. These numerous appendages enable some prokaryotes to attach to surfaces or to other prokaryotes (colorized TEM).
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Neisseria gonorrhoeae, the bacterium that causes gonorrhea, uses fimbriae to fasten itself to the mucous membranes of its host.

  • Specialized pili, called sex pili, link prokaryotes during conjugation, a process in which one cell transfers DNA to another cell (see Figure 18.17).
  • Most motile bacteria propel themselves by flagella that are structurally and functionally different from eukaryotic flagella
  • In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away from certain stimuli

Video: Prokaryotic Flagella (Salmonella typhimurium)

  • About half of all prokaryotes are capable of directional movement.Of the various structures that enable prokaryotes to move, the most common are flagella, which may be scattered over the entire cell surface or concentrated at one or both ends of the cell.
  • The flagella of prokaryotes differ from those of eukaryotes in both structure and mechanism of propulsion (Figure 27.6) .

Prokaryotic flagella are one–tenth the width of eukaryotic flagella and are not covered by an extension of the plasma membrane (see Figures 6.24 and 6.25 to review eukaryotic flagella).Figure 27.6 Prokaryotic flagellum. The motor of the prokaryotic flagellum is the basal apparatus, a system of rings embedded in the cell wall and plasma membrane (TEM). ATP–driven pumps transport protons out of the cell, and the diffusion of protons back into the cell powers the basal apparatus, which turns a curved hook. The hook is attached to a filament composed of chains of flagellin, a globular protein. (This diagram shows flagellar structures characteristic of gram–negative bacteria.)

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Cell wall


Basal apparatus




In a relatively uniform environment, flagellated prokaryotes may move randomly. In a heterogeneous environment, however, many prokaryotes exhibit taxis, movement toward or away from a stimulus (from the Greek taxis, to arrange). For example, prokaryotes that exhibit chemotaxis respond to chemicals by changing their movement pattern. They may move toward nutrients or oxygen (positive chemotaxis) or away from a toxic substance (negative chemotaxis). In 2003, scientists at Princeton University and the Institut Curie in Paris demonstrated that solitary E. coli cells exhibit positive chemotaxis toward other members of their species, enabling the formation of colonies

internal and genomic organization
Internal and Genomic Organization
  • Prokaryotic cells usually lack complex compartmentalization
  • Some prokaryotes do have specialized membranes that perform metabolic functions
  • These membranes are usually infoldings of the plasma membrane.
internal and genomic organization1
Internal and Genomic Organization
  • Figure 27.7 Specialized membranes of prokaryotes. (a) Infoldings of the plasma membrane, reminiscent of the cristae of mitochondria, function in cellular respiration in some aerobic prokaryotes (TEM). (b) Photosynthetic prokaryotes called cyanobacteria have thylakoid membranes, much like those in chloroplasts (TEM).
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Photosynthetic prokaryote

Aerobic prokaryote


The genome of a prokaryote is structurally very different from a eukaryotic genome and has on average only about one–thousandth as much DNA.

  • In the majority of prokaryotes, most of the genome consists of a ring of DNA that has relatively few proteins associated with it.
  • This ring of genetic material is usually called the prokaryotic chromosome (Figure 27.8) .
  • Unlike eukaryotic chromosomes, which are contained within the nucleus, the prokaryotic chromosome is located in a nucleoid region, a part of the cytoplasm that appears lighter than the surrounding cytoplasm in electron micrographs.
The typical prokaryotic genome is a ring of DNA that is not surrounded by a membrane and that is located in a nucleoid region

Figure 27.8 A prokaryotic chromosome. The thin, tangled loops surrounding this ruptured E. coli cell are parts of a single ring of DNA (colorized TEM).

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Some species of bacteria also have smaller rings of DNA called plasmids most consisting of only a few genes.
  • The plasmid genes provide resistance to antibiotics,
  • direct the metabolism of rarely encountered nutrients, or have other such “contingency” functions.

In most environments, the prokaryotic cell can survive without its plasmids, since all essential functions are encoded by the chromosome.

  • But in certain circumstances, such as when antibiotics are used to treat an infection, the presence of a plasmid can significantly increase a prokaryote′s chance of survival.
  • Plasmids replicate independently of the main chromosome, and many can be readily transferred between partners when prokaryotes conjugate (see Figure 18.18).

As explained in Chapters 16 and 17, DNA replication, transcription, and translation are fundamentally similar in prokaryotes and eukaryotes, although there are some differences.

  • For example, prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes and differ in their protein and RNA content.
  • These differences are great enough that certain antibiotics, such as erythromycin and tetracycline, bind to ribosomes and block protein synthesis in prokaryotes but not in eukaryotes. As a result, we can use these antibiotics to kill bacteria without harming ourselves.
reproduction and adaptation
Reproduction and Adaptation
  • Prokaryotes reproduce quickly by binary fission and can divide every 1–3 hours
  • Many prokaryotes form endospores, which can remain viable in harsh conditions for centuries
reproduction and adaptation1
Reproduction and Adaptation
  • Prokaryotes are highly successful in part because of their potential to reproduce quickly in a favorable environment.
  • Dividing by binary fission (see Figure 12.11), a single prokaryotic cell becomes 2 cells, which then become 4, 8, 16, and so on.
  • While most prokaryotes can divide every 1–3 hours, some species can produce a new generation in only 20 minutes under optimal conditions.

If reproduction continued unchecked at this rate, a single prokaryote could give rise to a colony outweighing Earth in only three days!

  • In reality, of course, prokaryotic reproduction is limited, as the cells eventually exhaust their nutrient supply, poison themselves with metabolic wastes, or are consumed by other organisms.
  • Prokaryotes in nature also face competition from other microorganisms, many of which produce antibiotic chemicals that slow prokaryotic reproduction.

The ability of some prokaryotes to withstand harsh conditions also contributes to their success.

  • Certain bacteria, for example, can form resistant cells called endospores when an essential nutrient is lacking in the environment (Figure 27.9) .
  • How?

The original cell produces a copy of its chromosome and surrounds it with a tough wall, forming the endospore.

  • Water is removed from the endospore, and metabolism inside it comes to a halt.
  • The rest of the original cell then disintegrates, leaving the endospore behind.
  • Most endospores are so durable that they can survive in boiling water.

Figure 27.9 An endospore. Bacillus anthracis, the bacterium that causes the deadly disease anthrax, produces endospores (TEM). An endospore′s thick, protective coat helps it survive in the soil for years.

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To kill endospores, microbiologists must heat their lab equipment with steam at 121°C under high pressure.

  • In less hostile environments, endospores can remain dormant but viable for centuries, able to rehydrate and resume metabolism when they receive cues that their environment has become more benign.

Prokaryotes can adapt quickly to changes in their environment through evolution by natural selection.

  • Because of prokaryotes′ rapid reproduction, mutations that confer greater fitness can swiftly become more common in a population.
  • .

For this reason, prokaryotes are important model organisms for scientists who study evolution in the laboratory.

  • The researchers regularly freeze samples of the colonies and later thaw them to compare their characteristics with those of later generations.
  • Such comparisons have revealed that the colonies today can grow 60% faster than the 1988 colonies under the same environmental conditions.

The rapid reproduction of E. coli enabled the scientists to document their adaptive evolution.Horizontal gene transfer (see Chapter 25) also facilitates rapid evolution in prokaryotes


For example, conjugation can permit the exchange of a plasmid containing a few genes or even large groups of genes.

  • Once the transferred genes are incorporated into a prokaryote′s genome, they are subject to natural selection during subsequent rounds of binary fission.
  • Horizontal gene transfer is a major force in the long–term evolution of pathogenic bacteria, a topic explored later in this chapter
Why do prokaryotes evolve amazingly fast?
  • Rapid reproduction and horizontal gene transfer facilitate the evolution of prokaryotes in changing environments
concept 27 2 a great diversity of nutritional and metabolic adaptations have evolved in prokaryotes
Concept 27.2: A great diversity of nutritional and metabolic adaptations have evolved in prokaryotes
  • All four models of nutrition are found among prokaryotes:
    • Photoautotrophy
    • Chemoautotrophy
    • Photoheterotrophy
    • Chemoheterotrophy

All organisms can be categorized by nutrition—how they obtain energy and carbon used in building the organic molecules that make up cells.

  • Nutritional diversity is greater among prokaryotes than among all eukaryotes:
  • Every type of nutrition observed in eukaryotes is represented among prokaryotes, along with some nutritional modes unique to prokaryotes.

Organisms that obtain energy from light are called phototrophs, and those that obtain energy from chemicals are called chemotrophs.

  • Organisms that need only the inorganic compound CO2 as a carbon source are called autotrophs . In contrast, heterotrophs require at least one organic nutrient—such as glucose—to make other organic compounds.
  • Combining these possibilities for energy sources and carbon sources results in four major modes of nutrition, described here and summarized in .Table 27.1

. Photoautotrophs are photosynthetic organisms that capture light energy and use it to drive the synthesis of organic compounds from CO2. Cyanobacteria and many other groups of prokaryotes are photoautotrophs, as are plants and algae.2. Chemoautotrophs also need only CO2 as a carbon source. However, instead of using light for energy, they oxidize inorganic substances, such as hydrogen sulfide (H2S), ammonia (NH3), or ferrous ions (Fe2+). This mode of nutrition is unique to certain prokaryotes.


3. Photoheterotrophs use light for energy but must obtain their carbon in organic form. A number of marine prokaryotes use this mode of nutrition.4. Chemoheterotrophs must consume organic molecules for both energy and carbon. This nutritional mode is found widely among prokaryotes as well as protists, fungi, animals, and even some parasitic plants.

metabolic relationships to oxygen
Metabolic Relationships to Oxygen
  • Prokaryotic metabolism also varies with respect to oxygen (see Chapter 9).
  • Obligate aerobes use O2 for cellular respiration and cannot grow without it.
  • Facultative anaerobes use O2 if it is present but can also grow by fermentation in an anaerobic environment.
  • Obligate anaerobes are poisoned by O2.

Some obligate anaerobes live exclusively by fermentation; others extract chemical energy by anaerobic respiration, in which substances other than O2, such as nitrate ions (NO3−) or sulfate ions (SO42−), accept electrons at the “downhill” end of electron transport chains

metabolic relationships to oxygen1
Metabolic Relationships to Oxygen
  • Prokaryotic metabolism varies with respect to oxygen:
    • Obligate aerobes require oxygen
    • Facultative anaerobes can survive with or without oxygen
    • Obligate anaerobes are poisoned by oxygen
nitrogen metabolism
Nitrogen Metabolism
  • Prokaryotes can metabolize nitrogen in a variety of ways
  • In nitrogen fixation, some prokaryotes convert atmospheric nitrogen to ammonia
nitrogen metabolism1
Nitrogen Metabolism
  • Nitrogen is essential for the production of amino acids and nucleic acids in all organisms. While eukaryotes are limited in the nitrogenous compounds they can use, prokaryotes can metabolize nitrogen in a wide variety of forms. For example, certain prokaryotes, including some cyanobacteria, convert atmospheric nitrogen (N2) to ammonia (NH3), a process called nitrogen fixation. The cells can then incorporate this “fixed” nitrogen into amino acids and other organic molecules. In terms of their nutrition, nitrogen–fixing cyanobacteria are the most self–sufficient of all organisms. They require only light, CO2, N2, water, and some minerals to grow. Chapter 54 discusses the essential roles that prokaryotes play in the nitrogen cycles of ecosystems
metabolic cooperation
Metabolic Cooperation
  • Cooperation between prokaryotes allows them to use environmental resources they could not use as individual cells
  • In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells exchange metabolic products

Video: Cyanobacteria (Oscillatoria)


Metabolic CooperationCooperation between prokaryotes allows them to use environmental resources they could not use as individual cells. In some cases, this cooperation takes place between specialized cells of a colony. For instance, the cyanobacterium Anabaena has genes encoding proteins for photosynthesis and for nitrogen fixation, but a single cell cannot carry out both processes at the same time. The reason is that photosynthesis produces O2, which inactivates the enzymes involved in nitrogen fixation. Instead of living as isolated cells, Anabaena forms filamentous colonies (Figure 27.10) . Most cells in a filament carry out only photosynthesis, while a few specialized cells called heterocysts carry out only nitrogen fixation. Heterocysts are surrounded by a thickened cell wall that restricts entry of O2 produced by neighboring photosynthetic cells. Intercellular connections allow heterocysts to transport fixed nitrogen to neighboring cells in exchange for carbohydrates.(Click image to enlarge) Figure 27.10 Metabolic cooperation in a colonial prokaryote. In the filamentous cyanobacterium Anabaena, cells known as heterocysts fix nitrogen, while the other cells carry out photosynthesis (LM). Anabaena is found in many freshwater lakes.In some prokaryotic species, metabolic cooperation occurs in surface–coating colonies known as biofilms(Figure 27.11) .Cells in a colony secrete signaling molecules that recruit nearby cells, causing the colony to grow. The cells also produce proteins that adhere the cells to the substrate and to one another. Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be expelled.(Click image to enlarge) Figure 27.11 A biofilm. The yellow mass in this colorized SEM is dental plaque, a biofilm that forms on tooth surfaces.Prokaryotes belonging to different species also cooperate. For example, sulfate–consuming bacteria and methane–consuming archaea coexist in ball–shaped aggregates on the ocean floor. The bacteria appear to use the archaea′s waste products, such as organic compounds and hydrogen. In turn, the bacteria produce compounds that facilitate methane consumption by the archaea. This partnership has global ramifications: Each year, these archaea consume an estimated 300 billion kg of methane, a major contributor to the greenhouse effect (see Chapter 54).

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In some prokaryotic species, metabolic cooperation occurs in surface-coating colonies called biofilms
concept 27 3 molecular systematics is illuminating prokaryotic phylogeny
Concept 27.3: Molecular systematics is illuminating prokaryotic phylogeny
  • Until the late 20th century, systematists based prokaryotic taxonomy on phenotypic criteria
  • Applying molecular systematics to the investigation of prokaryotic phylogeny has produced dramatic results

Molecular systematics is illuminating prokaryotic phylogenyUntil the late 20th century, systematists based prokaryotic taxonomy on phenotypic criteria such as shape, motility, nutritional mode, and response to Gram staining. These criteria are still valuable in certain contexts, such as the rapid identification of pathogenic bacteria cultured from a patient′s blood. But when it comes to prokaryotic phylogeny, comparing these characteristics does not reveal a clear history. Applying molecular systematics to the investigation of prokaryotic phylogeny, however, has produced dramatic results

lessons from molecular systematics
Lessons from Molecular Systematics
  • Molecular systematics is leading to a phylogenetic classification of prokaryotes
  • It allows systematists to identify major new clades
A tentative phylogeny of some of the major taxa of prokaryotes based on molecular systematics

Lessons from Molecular SystematicsAs discussed in Chapter 25, microbiologists began comparing the sequences of prokaryotic genes in the 1970s. Using small–subunit ribosomal RNA (SSU–rRNA) as a marker for evolutionary relationships, Carl Woese and his colleagues concluded that many prokaryotes once classified as bacteria are actually more closely related to eukaryotes and belong in a domain of their own—Archaea. Microbiologists have since analyzed larger amounts of genetic data—in some cases, entire genomes—and have concluded that a few traditional taxonomic groups, such as cyanobacteria, are in fact monophyletic. However, other groups, such as gram–negative bacteria, are scattered throughout several lineages. Figure 27.12 shows a tentative phylogeny of some of the major taxa of prokaryotes based on molecular systematics.(Click image to enlarge) Figure 27.12 A simplified phylogeny of prokaryotes. This phylogenetic tree based on molecular data highlights the relationships between the major prokaryotic groups discussed in this chapter.Prokaryotic phylogeny is still a work in progress, but two important lessons have already emerged. One is that the genetic diversity of prokaryotes is immense. When researchers began to sequence the genes of prokaryotes, they could investigate only those species that could be cultured in the laboratory—a small minority of all prokaryotic species. Methods pioneered by Norman Pace of the University of Colorado in the 1980s now allow researchers to sample genetic material directly from the environment. Every year this “genetic prospecting” adds major new branches to the tree of life. (Some researchers suggest that certain branches represent entire new kingdoms.) While only 4,500 prokaryotic species have been fully characterized, a single handful of soil could contain 10,000 prokaryotic species, according to some estimates. You can see why taking full stock of this diversity will require many years of research.Another important lesson is the apparent significance of horizontal gene transfer in the evolution of prokaryotes. Over hundreds of millions of years, prokaryotes have acquired genes from distantly related species, and they continue to do so today. As a result, significant portions of the genomes of many prokaryotes are actually mosaics of genes imported from other species.Note again in Figure 27.12 a key inference based on molecular systematics: the very early divergence of prokaryotes into two main lineages, bacteria and archaea

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Domain Bacteria

















Universal ancestor

  • Diverse nutritional types are scattered among the major groups of bacteria
  • The two largest groups are the proteobacteria and the Gram-positive bacteria
  • Every major mode of nutrition and metabolism is represented among bacteria, and even a small taxonomic group of bacteria may contain species exhibiting many different nutritional modes. Examine Figure 27.13 on the following pages for a closer look at several major groups of bacteria.a. b
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Subgroup: Alpha Proteobacteria

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Chlamydia (arrows)

Rhizobium (arrows)


Subgroup: Beta Proteobacteria

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Subgroup: Gamma Proteobacteria

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Mycoplasmas covering

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Subgroup: Delta Proteobacteria

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Subgroup: Epsilon Proteobacteria

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Heliocobacter pylori

  • Archaea share certain traits with bacteria and other traits with eukaryotes
  • However, archaea also have many unique characteristics, as we would expect for a taxon that has followed a separate evolutionary path for so long
  • Archaea share certain traits with bacteria and other traits with eukaryotes (Table 27.2) . Table 27.2 A Comparison of the Three Domains of Life.

The first prokaryotes that were classified in domain Archaea are species that live in environments so extreme that few other organisms can survive there.

  • Such organisms are known as extremophiles, meaning “lovers” of extreme conditions (from the Greek philos, lover).
  • Extremophiles include extreme thermophiles, extreme halophiles, and methanogens.

Extreme thermophiles (from the Greek thermos, hot) thrive in very hot environments (see Figure 27.1).

  • For example, archaea in the genus Sulfolobus live in sulfur–rich volcanic springs at temperatures up to 90°C.
  • Pyrolobus fumarii, an extreme thermophile found around deep–sea hydrothermal vents on the Mid–Atlantic Ridge, can survive at temperatures as high as 113°C. Another extreme thermophile, Pyrococcus furiosus, is used in biotechnology as a source of DNA polymerase for the polymerase chain reaction (PCR) technique (see Chapter 20).

Extreme halophiles (from the Greek halo, salt) live in highly saline environments, such as the Great Salt Lake and the Dead Sea.

  • Colonies of certain extreme halophiles form a purple–red scum that owes its color to bacteriorhodopsin, a photosynthetic pigment very similar to the visual pigments in the vertebrate retina (Figure 27.14) .Figure 27.14 Extreme halophiles. Colorful “salt–loving” archaea thrive in these ponds near San Francisco. Used for commercial salt production, the ponds contain water that is five to six times as salty as seawater.

Methanogens are named for the unique way they obtain energy: They use CO2 to oxidize H2, releasing methane as a waste product.

  • Among the strictest of anaerobes, methanogens are poisoned by O2.
  • Some species live in swamps and marshes where other microorganisms have consumed all the O2. The “marsh gas” found in such environments is the methane produced by these archaea.

Other species of methanogens inhabit the anaerobic environment within the guts of cattle, termites, and other herbivores, playing an essential role in the nutrition of these animals.

  • Methanogens are also important decomposers in sewage treatment facilities.

All known extreme halophiles and methanogens are members of a clade called Euryarchaeota (from the Greek eurys, broad, a reference to the habitat range of these prokaryotes). Euryarchaeota also includes some extreme thermophiles,

  • Most thermophilic species belong to a second clade, Crenarchaeota(cren means “spring,” as in hydrothermal springs).
Some archaea live in extreme environments
  • Extreme thermophiles thrive in very hot environments
  • Extreme halophiles live in high saline environments
concept 27 4 prokaryotes play crucial roles in the biosphere
Concept 27.4: Prokaryotes play crucial roles in the biosphere
  • Prokaryotes are so important to the biosphere that if they were to disappear, the prospects for any other life surviving would be dim
  • If humans were to disappear from the planet tomorrow, life on Earth would go on for most other species.
chemical recycling
Chemical Recycling
  • The atoms that make up the organic molecules in all living things were at one time part of inorganic compounds in the soil, air, and water.
  • Sooner or later, where those atoms will return?
  • Ecosystems depend on the continual recycling of chemical elements between the living and nonliving components of the environment, and prokaryotes play a major role in this process.

For example, chemoheterotrophicprokaryotes function as decomposers, breaking down corpses, dead vegetation, and waste products, thereby unlocking supplies of carbon, nitrogen, and other elements. (See Chapter 54 for a detailed discussion of chemical cycles.)


Prokaryotes also convert inorganic compounds into forms that can be taken up by other organisms.

  • Autotrophic prokaryotes, for example, use CO2 to make organic compounds, which are then passed up through food chains. Cyanobacteria produce atmospheric O2,
  • Some species also fix nitrogen into a form that other organisms can use to make proteins
chemical recycling1
Chemical Recycling
  • Prokaryotes play a major role in the continual recycling of chemical elements between the living and nonliving components of ecosystems
  • Chemoheterotrophic prokaryotes function as decomposers, breaking down corpses, dead vegetation, and waste products
  • Nitrogen-fixing prokaryotes add usable nitrogen to the environment
symbiotic relationships
Symbiotic Relationships
  • Many prokaryotes live with other organisms in symbiotic relationships
  • In mutualism, both symbiotic organisms benefit
  • In commensalism, one organism benefits while neither harming nor helping the other in any significant way
  • In parasitism, one organism, called a parasite, benefits at the expense of the host
symbiotic relationships1
Symbiotic Relationships
  • Just as certain species of prokaryotes have beneficial associations with other prokaryotes (metabolic cooperation), some prokaryotes form similarly intimate relationships with eukaryotes.
  • An ecological relationship between organisms of different species that are in direct contact is calledsymbiosis (from a Greek word meaning “living together”).

If one of the symbiotic organisms is much larger than the other, the larger is known as the hostand the smaller is known as the symbiont.

  • Symbiotic relationships are categorized as either mutualism, commensalism, or parasitism.

In mutualism, both symbiotic organisms benefit (Figure 27.15) .

  • In commensalism, one organism benefits while neither harming nor helping the other in any significant way. (Commensalism is rare in nature, as further discussed in Chapter 53.)
  • In parasitism, one organism, called a parasite, benefits at the expense of the host.

Figure 27.15 Mutualism: bacterial “headlights.” The glowing oval below the eye of the flashlight fish (Photoblepharon palpebratus) is an organ harboring bioluminescent bacteria. The fish uses the light to attract prey and to signal potential mates. The bacteria receive nutrients from the fish.


The well–being of many eukaryotes—yourself included—depends on mutualistic prokaryotes.

  • For example, human intestines are home to an estimated 500 to 1,000 species of bacteria; their cells outnumber all human cells in the body by as much as ten times.
  • Many of these species are mutualists, digesting food that our own intestines cannot break down
concept 27 5 prokaryotes have both harmful and beneficial impacts on humans
Concept 27.5: Prokaryotes have both harmful and beneficial impacts on humans
  • Some prokaryotes are human pathogens, but others have positive interactions with humans
prokaryotes have both harmful and beneficial impacts on humans
Prokaryotes have both harmful and beneficial impacts on humans
  • While the best–known prokaryotes tend to be those that cause illness in humans, these pathogens represent only a small fraction of prokaryotic species. Many other prokaryotes have positive interactions with humans, even serving as essential tools in agriculture and industry
pathogenic prokaryotes
Pathogenic Prokaryotes
  • The prokaryotic species that are human parasites deserve their negative reputation.
  • All told, prokaryotes cause about half of all human diseases.
  • Between 2 and 3 million people a year die of the lung disease tuberculosis, which is caused by the bacillus Mycobacterium tuberculosis, while another 2 million die from various diarrheal diseases caused by other prokaryotes.

In the United States, the most widespread pest–carried disease is Lyme disease (Figure 27.16) .

  • Caused by a bacterium carried by ticks that live on deer and field mice, Lyme disease can produce debilitating arthritis, heart disease, and nervous disorders if untreated.

Figure 27.16 Lyme disease. Ticks in the genus Ixodes spread the disease by transmitting the spirochete Borrelia burgdorferi (colorized SEM).

  • A large, ring–shaped rash may develop at the site of the tick′s bite, as shown in the photograph of a person′s lower leg.
Pathogenic prokaryotes typically cause disease by releasing exotoxins or endotoxins
  • Exotoxins cause disease even if the prokaryotes that produce them are not present
  • Endotoxins are released only when bacteria die and their cell walls break down
  • Many pathogenic bacteria are potential weapons of bioterrorism
some detail on exotoxins and endotoxins
Some detail on exotoxins and endotoxins…
  • Exotoxins are proteins secreted by prokaryotes.
  • Cholera, a dangerous diarrheal disease, is caused by an exotoxin released by the proteobacterium Vibrio cholerae. The exotoxin stimulates intestinal cells to release chloride ions into the gut, and water follows by osmosis.

Exotoxins can produce disease even if the prokaryotes that manufacture them are not present.

  • For example, the fatal disease botulism is caused by botulinum toxin, an exotoxin secreted by the gram–positive bacterium Clostridium botulinumas it ferments improperly canned foods.

Endotoxinsare lipopolysaccharide components of the outer membrane of gram–negative bacteria.

  • In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell walls break down.

Examples of endotoxin–producing bacteria include nearly all species in the genus Salmonella, which are not normally present in healthy animals.

  • Salmonella typhi causes typhoid fever, and several other Salmonella species, some of which are frequently found in poultry, cause food poisoning.

Since the 19th century, improvements in sanitation in the developed world have greatly reduced the threat of pathogenic prokaryotes.

  • Antibiotics have saved a great many lives and reduced the incidence of disease.
  • However, resistance to antibiotics is currently evolving in many strains of prokaryotes.

As you read earlier, the rapid reproduction of prokaryotes enables genes conferring resistance to multiply quickly throughout prokaryotic populations as a result of natural selection,and these genes can spread to other species by horizontal gene transfer.


Horizontal gene transfer can also spread genes associatedwith virulence, turning normally harmless prokaryotes into fatal pathogens.

  • E. coli, for instance, is ordinarily a harmless symbiont in the human intestines, but pathogenic strains that cause bloody diarrhea have emerged. One of the most dangerous strains, called O157:H7, first came to the attention of microbiologists in 1982. Today it is a global threat;

In the United States alone there are 75,000 cases of O157:H7 infection per year, often from contaminated beef. In 2001, an international team of scientists sequenced the genome of O157:H7 and compared it with the genome of a harmless strain of E. coli called K–12. They discovered that 1,387 out of the 5,416 genes in O157:H7 have no counterpart in K–12. These 1,387 genes must have been incorporated into the genome of O157:H7 through horizontal gene transfer, most likely through the action of bacteriophages (see Figure 18.16). Many of the imported genes are associated with the pathogenic bacterium′s invasion of its host. For example, some genes code for exotoxins that enable O157:H7 to attach itself to the intestinal wall and extract nutrients.


Pathogenic prokaryotes pose a potential threat asweapons of bioterrorism.

  • In October 2001, endospores of Bacillus anthracis, the bacterium that causes anthrax, were found in envelopes mailed to members of news media and the U.S. Senate.
  • Eighteen people developed cases of anthrax, and five died.

Other prokaryotes that could be candidates as weapons include C. botulinum and Yersinia pestis, which causes plague.

  • The threat has stimulated intense research on pathogenic prokaryotic species. In May 2003, scientists at the Institute for Genomic Research in Maryland published the complete genome of the strain of B. anthracis that had been used in the October 2001 attack, in the hope of developing new vaccines and antibiotics
prokaryotes in research and technology
Prokaryotes in Research and Technology
  • Experiments using prokaryotes have led to important advances in DNA technology
  • Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment
Some other uses of prokaryotes:
    • Recovery of metals from ores
    • Synthesis of vitamins
    • Production of antibiotics, hormones, and other products
prokaryotes in research and technology1
Prokaryotes in Research and Technology
  • On a positive note, we reap many benefits from the metabolic capabilities of prokaryotes.
  • For example, humans have long used bacteria to convert milk to cheese and yogurt.
  • In recent years, our greater understanding of prokaryotes has led to an explosion of new applications in biotechnology; the use of E. coli in gene cloning and of Agrobacterium tumefaciens in producing transgenic plants are two examples (see Chapter 20).

Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from soil, air, or water.

  • For example, anaerobic bacteria and archaea decompose the organic matter in sewage, converting it to material that can be used as landfill or fertilizer after chemical sterilization.
  • Other bioremediation applications include breaking down radioactive waste and cleaning up oil spills (Figure 27.17) .(Click image to enlarge)

Figure 27.17 Bioremediation of an oil spill. A worker sprays fertilizers on an oil–soaked beach in Alaska. The fertilizers stimulate growth of native bacteria that initiate the breakdown of the oil—in some cases, speeding the natural breakdown process fivefold.


In the mining industry, prokaryotes help recover metals from ores.

  • Bacteria assist in extracting over 30 billion kg of copper from copper sulfides each year.
  • Harnessing other prokaryotes that can extract gold from ore, one factory in the African nation of Ghana processes 1 million kg of gold concentrate a day—about half of Ghana′s foreign exchange.

Through genetic engineering, humans can now modify prokaryotes to produce vitamins, antibiotics, hormones, and other products (see Chapter 20).


One of the most radical ideas for modifying prokaryotes has come from Craig Venter (one of the leaders of the Human Genome Project), who has announced that he and his colleagues are attempting to build “synthetic chromosomes” for prokaryotes—in effect, producing entirely new species from scratch. Venter hopes to “design” prokaryotes that can perform specific tasks, such as producing large amounts of hydrogen to reduce dependence on fossil fuels.


The usefulness of prokaryotes largely derives from their diverse forms of nutrition and metabolism.

  • All this metabolic versatility evolved prior to the appearance of the structural novelties that heralded the evolution of eukaryotic organisms, the topic of the remainder of this unit