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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Their collective biological mass (biomass) is at least ten times that of all eukaryotes.
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.
Structural, functional, and genetic adaptations contribute to prokaryotic successMost prokaryotes are unicellular, although some species aggregate transiently or permanently in colonies.
Prokaryotic cells have a variety of shapes, the three most common of which are spheres (cocci), rods (bacilli), and spirals (Figure 27.2) .
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).
The cell walls of prokaryotes differ in molecular composition and construction from those of eukaryotes.
Archaean cell walls contain a variety of polysaccharides and proteins but lack peptidoglycan.
(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).
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.
Neisseria gonorrhoeae, the bacterium that causes gonorrhea, uses fimbriae to fasten itself to the mucous membranes of its host.
Video: Prokaryotic Flagella (Salmonella typhimurium)
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.)
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
The genome of a prokaryote is structurally very different from a eukaryotic genome and has on average only about one–thousandth as much DNA.
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).
In most environments, the prokaryotic cell can survive without its plasmids, since all essential functions are encoded by the chromosome.
As explained in Chapters 16 and 17, DNA replication, transcription, and translation are fundamentally similar in prokaryotes and eukaryotes, although there are some differences.
If reproduction continued unchecked at this rate, a single prokaryote could give rise to a colony outweighing Earth in only three days!
The ability of some prokaryotes to withstand harsh conditions also contributes to their success.
The original cell produces a copy of its chromosome and surrounds it with a tough wall, forming the endospore.
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.
To kill endospores, microbiologists must heat their lab equipment with steam at 121°C under high pressure.
Prokaryotes can adapt quickly to changes in their environment through evolution by natural selection.
For this reason, prokaryotes are important model organisms for scientists who study evolution in the laboratory.
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.
All organisms can be categorized by nutrition—how they obtain energy and carbon used in building the organic molecules that make up cells.
Organisms that obtain energy from light are called phototrophs, and those that obtain energy from chemicals are called chemotrophs.
. 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.
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
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).
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 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
Subgroup: Alpha Proteobacteria
Subgroup: Beta Proteobacteria
Subgroup: Gamma Proteobacteria
a human fibroblast cell
Subgroup: Delta Proteobacteria
Subgroup: Epsilon Proteobacteria
The first prokaryotes that were classified in domain Archaea are species that live in environments so extreme that few other organisms can survive there.
Extreme thermophiles (from the Greek thermos, hot) thrive in very hot environments (see Figure 27.1).
Extreme halophiles (from the Greek halo, salt) live in highly saline environments, such as the Great Salt Lake and the Dead Sea.
Methanogens are named for the unique way they obtain energy: They use CO2 to oxidize H2, releasing methane as a waste product.
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.
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,
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.
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.
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.
In the United States, the most widespread pest–carried disease is Lyme disease (Figure 27.16) .
Figure 27.16 Lyme disease. Ticks in the genus Ixodes spread the disease by transmitting the spirochete Borrelia burgdorferi (colorized SEM).
Exotoxins can produce disease even if the prokaryotes that manufacture them are not present.
Endotoxinsare lipopolysaccharide components of the outer membrane of gram–negative bacteria.
Examples of endotoxin–producing bacteria include nearly all species in the genus Salmonella, which are not normally present in healthy animals.
Since the 19th century, improvements in sanitation in the developed world have greatly reduced the threat of pathogenic 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.
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.
Other prokaryotes that could be candidates as weapons include C. botulinum and Yersinia pestis, which causes plague.
Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from soil, air, or water.
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.
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.