1. Bacteria and Archaea: The Prokaryotic Domains

2. Bacteria and Archaea: The Prokaryotic Domains
Why Three Domains?
General Biology of the Prokaryotes
Prokaryotes in Their Environments
Prokaryote Phylogeny and Diversity
The Bacteria
The Archaea

3. Why Three Domains?
Biologists now categorize all life into three domains: Bacteria, Archaea, and Eukarya.
Members of all three domains have certain characteristics in common:
They conduct glycolysis.
They replicate their DNA semiconservatively.
They have DNA that encodes polypeptides.
They produce polypeptides by transcription and translation and use the same genetic code.
They have plasma membranes and ribosomes.

4. Why Three Domains?
All three domains had a single common ancestor.
Present-day Archaea share a more recent common ancestor with eukaryotes than they do with bacteria.
The common ancestor of all three domains was prokaryotic.
It likely had a circular chromosome and structural genes organized into operons.
The three domains are products of billions of years of natural selection. Prokaryotes were the only life-forms for billions of years.

5. Figure 27.2 The Three Domains of the Living World

6. General Biology of the Prokaryotes
Prokaryotes live all around and even within us.
Prokaryotes are important to the biosphere:
Some perform key steps in the cycling of nitrogen, sulfur, and carbon.
Some trap energy from the sun and from inorganic chemical sources.
Some help animals digest their food.

7. General Biology of the Prokaryotes
Prokaryotes are found in every conceivable habitat on the planet.
They live at extremely hot temperatures.
They can survive extreme alkalinity and saltiness.
Some survive in the presence of oxygen, while others survive without it.
Some live at the bottom of the sea.
Some live in rocks more than 2 km into Earth’s solid crust.

8. General Biology of the Prokaryotes
Three shapes are common to prokaryotes: spheres, rods, and curved or spiral forms.
Spherical prokaryotes are called cocci (singular coccus). Cocci live singly or in two- or three- dimensional arrays of chains, plates, or blocks.
Rod-shaped prokaryotes are called bacilli. These live in chains or singularly.
Chains (filaments) and other associations do not signify multicellularity because each cell is viable independently.

9. Figure 27.3 Shapes of Prokaryotic Cells

10. General Biology of the Prokaryotes
The prokaryotic cell differs from the eukaryotic cell in three important ways:
The DNA of the prokaryotic cell is not organized within a membrane-enclosed nucleus.
Prokaryotes have no membrane-enclosed cytoplasmic organelles. Some do have plasma membrane infoldings.
Prokaryotes lack a cytoskeleton and thus do not divide by mitosis. Instead, they divide by fission after replicating their DNA.

11. General Biology of the Prokaryotes
Some prokaryotes are motile.
Some spiral bacteria called spirochetes use a rolling motion made possible by modified flagella called axial filaments.
Many cyanobacteria and some other bacteria use a gliding mechanism.
Some aquatic prokaryotes move slowly up and down in the water by adjusting the amount of gas in gas vesicles.
The most common type of locomotion is driven by flagella.

12. Figure 27.4 Structures Associated with Prokaryote Motility (Part 1)

13. Figure 27.4 Structures Associated with Prokaryote Motility (Part 2)

14. General Biology of the Prokaryotes
Bacterial flagella consist of a single fibril made of the protein flagellin projecting from the surface, plus a hook and basal body.
The structure of the bacterial flagellum is entirely different from the eukaryotic flagellum.
In addition, the prokaryotic flagellum rotates about its base, rather than beating, as a eukaryotic flagellum does.

15. Figure 27.5 Some Bacteria Use Flagella for Locomotion

16. General Biology of the Prokaryotes
Most prokaryotes have a thick and stiff cell wall containing peptidoglycan.
Peptidoglycan is unique to bacteria.
The Gram stain, developed by Hans Christian Gram in 1884, separates bacteria into two distinct groups based on the nature of their cell walls.

17. General Biology of the Prokaryotes
In a Gram stain, cells are soaked in violet dye and treated with iodine, then washed with alcohol and counterstained with safranine.
Gram-positive bacteria stain violet. Gram-negative bacteria stain pink to red.
Gram-positive cell walls have a thick layer of peptidoglycan.
Gram-negative cell walls have a second membrane outside the cell wall, and the cell wall has less peptidoglycan.
The space between the outer membrane and the cell wall is called the periplasmic space.

18. Figure 27.6 The Gram Stain and the Bacterial Cell Wall (Part 1)

19. Figure 27.6 The Gram Stain and the Bacterial Cell Wall (Part 2)

20. General Biology of the Prokaryotes
Different features of the cell wall contribute to disease-causing characteristics of some prokaryotes.
Many antibiotics act by disrupting cell-wall synthesis and tend to have little or no effect on eukaryotic cells.

21. General Biology of the Prokaryotes
Prokaryotes reproduce asexually by fission.
However, prokaryotes can exchange genetic material through transformation, conjugation, and transduction.
Rates of division vary with species:
E. coli divides about once every 20 minutes.
The shortest known generation time for prokaryotes is about 10 minutes.
Bacteria living deep in Earth’s crust might not divide for as long as 100 years.

22. General Biology of the Prokaryotes
The long evolutionary history of bacteria and archaea has led to a diversity of metabolic pathways.
Obligate anaerobes live only in the absence of oxygen. Oxygen is toxic to them.
Facultative anaerobes can shift between anaerobic metabolism (such as fermentation) and the aerobic mode (cellular respiration).
Aerotolerant anaerobes cannot conduct cellular respiration, but are not damaged by oxygen when it is present.
Obligate aerobes are unable to survive for extended periods in the absence of oxygen.

23. General Biology of the Prokaryotes
There are four nutritional categories among prokaryotes:
Photoautotrophs
Photoheterotrophs
Chemoautotrophs
Chemoheterotrophs

24. General Biology of the Prokaryotes
Photoautotrophs are photosynthesizers, using light for energy and CO2 as a carbon source
Cyanobacteria use chlorophyll a and produce oxygen as a byproduct.
Other photosynthetic bacteria use bacteriochlorophyll and do not produce O2. Some use H2S instead of H2O as an electron donor and produce particles of pure sulfur.
Bacteriochlorophyll absorbs longer wavelengths than other chlorophylls do. This longer wavelength of light penetrates farther into water and is not absorbed by plants.

25. Figure 27.7 Bacteriochlorophyll Absorbs Long-Wavelength Light

26. General Biology of the Prokaryotes
Photoheterotrophs use light as a source of energy but must get carbon from other organisms.
They use carbohydrates, fatty acids, and alcohols for carbon.
Purple nonsulfur bacteria are photoheterotrophs.

27. General Biology of the Prokaryotes
Chemolithotrophs obtain energy from oxidizing inorganic substances and use some of the energy to fix CO2.
Some use pathways to fix CO2 identical to those of the Calvin cycle.
Others oxidize ammonia, hydrogen gas, hydrogen sulfide, sulfur, or methane.
Some deep-sea ecosystems around thermal vents are based on chemolithotrophs, which form the basis for a food chain that includes giant worms, crabs, and mollusks.

28. General Biology of the Prokaryotes
Chemoheterotrophs typically obtain energy and carbon atoms from one or more organic compounds.
Most known bacteria and archaea are chemoheterotrophs, as are all animals, fungi, and many protists.

29. General Biology of the Prokaryotes
Some bacteria use oxidized inorganic ions, such as nitrate, nitrite, or sulfate, as electron acceptors.
Denitrifiers are normally aerobic bacteria, mostly Bacillus and Pseudomonas.
Under anaerobic conditions they use NO3- in place of oxygen as an electron acceptor.
They release nitrogen to the atmosphere as N2 gas.

30. General Biology of the Prokaryotes
Nitrogen fixers convert atmospheric N2 gas into ammonia by means of the following reaction:
N2 + 6 H ® 2 NH3
All organisms require fixed nitrogen for their proteins, nucleic acids, and other nitrogen- containing compounds.
Only archaea and bacteria, including some cyanobacteria, can fix nitrogen.

31. General Biology of the Prokaryotes
Bacteria of two genera, Nitrosomonas and Nitrosococcus, are nitrifiers, meaning that they convert ammonia to nitrite.
Nitrobacter is a nitrifier that oxidizes nitrite to nitrate.
Chemosynthesis in these bacteria is powered by the energy released by the oxidation process.

32. Prokaryotes in Their Environments
Prokaryotes are important in element cycling.
Plants depend on prokaryotic nitrogen-fixers for their nutrition.
Denitrifiers prevent accumulation of toxic levels of nitrogen in lakes and oceans.
Cyanobacteria have had a powerful effect on changing Earth by generating atmospheric O2.
The accumulation of O2 in the atmosphere made the evolution of more efficient glucose metabolism possible and caused the extinction of many species that couldn’t tolerate oxygen.

33. Prokaryotes in Their Environments
Archaea help stave off global warming.
There are ten trillion tons of methane lying deep under the ocean floor.
Archaea present at the bottom of the seas metabolize this methane as it rises from its deposits, preventing it from hastening global warming.

34. Prokaryotes in Their Environments
Prokaryotes live on and in other organisms:
Mitochondria and chloroplasts are assumed to be descendants of free-living bacteria.
Plants and bacteria form cooperative nitrogen-fixing nodules on the plant roots.
The tsetse fly obtains the vitamins needed for reproduction from a bacterium living inside its cells.
Cows depend on prokaryotes in their digestive tract to digest cellulose.
Humans use vitamins B12 and K produced by our intestinal bacteria.

35. Prokaryotes in Their Environments
Koch’s postulates, or rules, for determining that a particular microorganism causes a particular disease:
The microorganism must always be found in individuals with the disease.
The microorganism can be taken from the host and grown in pure culture.
A sample of the culture produces the disease when injected into a new, healthy host.
The newly infected host yields a new, pure culture of microorganisms.

36. Prokaryotes in Their Environments
Only a tiny proportion of prokaryotic species are pathogens. All known prokaryotic pathogens are Bacteria (not Archaea).
For an organism to be a pathogen, it must:
Arrive at the body surface.
Enter the body.
Evade detection and defenses.
Multiply inside the host.
Infect new hosts.

37. Prokaryotes in Their Environments
For the host, the seriousness of the infection depends on the invasiveness and the toxigenicity of the pathogen.
Corynebacterium diphtheriae, the agent that causes diphtheria, has low invasiveness but produces powerful toxins.
Bacillus anthracis, which causes anthrax, has low toxigenicity, but is so invasive that the bloodstream of infected animals teems with organisms.

38. Prokaryotes in Their Environments
There are two major types of toxins:
Endotoxins, such those produced by Salmonella and Escherichia are lipopolysaccharides from the outer membrane of Gram-negative bacteria. They are released when the bacteria grow or lyse.
Exotoxins, which are produced and released by living, multiplying bacteria, can be highly toxic, even fatal.
Tetanus, botulism, cholera, and plague are all examples of exotoxins.

39. Prokaryotes in Their Environments
Many unicellular microorganisms, prokaryotes in particular, form dense films called biofilms.
The cells lay down a gel-like polysaccharide matrix when they contact a solid surface.This matrix traps other bacteria, forming a biofilm.
Biofilms can make bacteria difficult to kill. Pathogenic bacteria may form a film that is impermeable to antibiotics, for example.
Biofilms can form on just about any available surface and are the object of much current research.

40. Prokaryote Phylogeny and Diversity
Classification schemes are used to help identify unknown organisms, reveal evolutionary relationships, and provide names for organisms.
In the past, phenotypic characters such as color, shape, antibiotic resistance, and staining were used to classify prokaryotes.
Now, nucleic acid sequencing is providing clues to evolutionary relationships.

41. Prokaryote Phylogeny and Diversity
Ribosomal RNA (rRNA) is particularly useful for evolutionary studies for several reasons:
rRNA is evolutionarily ancient.
All organisms have rRNA.
rRNA functions the same way in all organisms.
rRNA changes slowly enough that sequence similarities between groups of organisms are easily found.

42. Prokaryote Phylogeny and Diversity
Lateral gene transfer among bacteria of different species has complicated the use of sequencing information for determining the evolutionary relationships of bacteria.
There is currently great controversy over prokaryotic phylogeny.

43. Figure 27.8 Two Domains: A Brief Overview

44. Prokaryote Phylogeny and Diversity
Mutations are a major source of prokaryotic variation.
The rapid multiplication of many prokaryotes— along with mutation, selection, and genetic drift— causes rapid changes.
Important changes, such as acquired resistance to antibiotics, can occur broadly in just a few years.

45. The Bacteria
The most well-studied prokaryotes are the bacteria.
Focus will be on five groups: the proteobacteria, cyanobacteria, spirochetes, chlamydias, and firmicutes.
Three of the bacterial groups that may have branched out earliest are thermophiles.

46. The Bacteria
The proteobacteria, or purple bacteria, make up the largest group in terms of the number of species.
Some are Gram-negative, bacteriochlorophyll- containing, and sulfur-using photoautotrophs. However, others have dramatically different phenotypes.
The mitochondria of eukaryotes were derived from proteobacteria by endosymbiosis.

47. The Bacteria
The common ancestor to all proteobacteria was probably a photoautotroph.
Early in evolutionary history, two of the five proteobacteria groups lost the ability to photosynthesize and became chemoheterotrophs.
There also are some chemolithotrophs and chemoheterotrophs in all three of the other groups.
Some fix nitrogen (Rhizobium) and some help cycle nitrogen and sulfur.

48. Figure 27.9 The Evolution of Metabolism in the Proteobacteria

49. The Bacteria
Cyanobacteria (blue-green bacteria) are photoautotrophs.
They use chlorophyll a for photosynthesis and release O2. Their photosynthesis was the basis of the transformation of Earth’s atmosphere.
Cyanobacteria have highly organized internal membranes called photosynthetic lamellae or thylakoids.
Chloroplasts are derived from an endosymbiotic cyanobacterium.
Some filamentous colonies differentiate into three cell types: vegetative cells, spores, and heterocysts (specialized for nitrogen fixation).

50. Figure 27.11 Cyanobacteria (Part 1)

51. Figure 27.11 Cyanobacteria (Part 2)

52. The Bacteria
Spirochetes are Gram-negative bacteria with axial filaments, which are fibrils running through the periplasmic space.
The cell body is a long cylinder coiled into a spiral.
Many spirochetes live in humans as parasites. A few are pathogens (e.g., those that cause syphilis and Lyme disease). Others live free in mud or water.

53. Figure A Spirochete

54. The Bacteria
Chlamydias are Gram-negative intracellular parasites that are among the smallest bacteria.
Their life cycle involves two different forms of cells: elementary bodies and reticulate bodies.
In humans, they cause eye infections, sexually transmitted disease, and some forms of pneumonia.

55. Figure 27.13 Chlamydias Change Form during Their Life Cycle

56. The Bacteria
Most firmicutes are Gram-positive, but some are Gram-negative, and some have no cell wall at all.
When a key nutrient becomes scarce, some produce endospores, which are heat-resistant resting structures.
The bacterium replicates its DNA and encapsulates one copy in a tough cell wall, thickened with peptidoglycan and covered with a spore coat.
The parent cell then breaks down, releasing the endospore.
Some endospores can be reactivated after more than a thousand years of dormancy.

57. Figure 27.14 The Endospore: A Structure for Waiting Out Bad Times

58. Figure 27.15 Gram-Positive Firmicutes

59. The Bacteria
Actinomycetes are firmicutes that develop an elaborately branched system of filaments.
Some reproduce by forming chains of spores at the tips of filaments.
In others, the filamentous growth ceases and the structure breaks up into typical cocci or bacilli, which then reproduce by fission.
Mycobacterium tuberculosis is an actinomycete.
Most of our antibiotics are derived from actinomycetes. Streptomyces produces the antibiotic streptomycin, as well as hundreds of other antibiotics.

60. Figure 27.16 Filaments of an Actinomycetes

61. The Bacteria
Mycoplasmas lack cell walls, are the smallest bacteria (some have a diameter of 0.2 µm), and have the least amount of DNA.
They may have the minimum amount of DNA necessary to code for the essential properties of a living cell.

62. Figure 27.17 The Tiniest Living Cells

63. The Archaea
The study of Archaea is still in its very early stages.
It is possible that the domain Archaea is paraphyletic.
Most archaea live in environments that are extreme in one way or another: temperature, salinity, oxygen concentration, or pH.
There are two groups of Archaea: Euryarchaeota and Crenarchaeota.

64. The Archaea
The Archaea lack peptidoglycan in their cell walls and have distinctive lipids in their cell membranes.
When biologists sequenced the first archaean genome, more than half of its 1,738 genes were unlike any found in the other two domains.
The unusual lipids in the membranes of archaea are long fatty acids bonded to glycerol via an ether linkage, as opposed to the ester linkage found in other organisms.

65. Figure 27.18 Membrane Architecture in Archaea

66. The Archaea
Most Crenarchaeota are both thermophilic and acidophilic.
Members of the genus Sulfolobus live in hot sulfur springs at temperatures of 70–75ºC and die at 55º C (131ºF).
They grow best at pH 2–pH 3 but can survive pH 0.9.

67. Figure 27.19 Some Would Call It Hell; Archaea Call It Home

68. The Archaea
Some species of Euryarchaeota are methanogens, producing methane (CH4) from CO2.
All methanogens are obligate anaerobes.
Methanogens release approximately 2 billion tons of methane gas into Earth’s atmosphere. About one-third of this comes from methanogens in the guts of grazing herbivores.
Methanopyrus lives on the ocean bottom near volcanic vents and can live at 110ºC.

69. The Archaea
Some Euryarchaeota, called extreme halophiles, live exclusively in very salty environments such as the Dead Sea or in pickle brine.
Some of these organisms survive a pH of 11.5.
Some of the extreme halophiles use the pigment retinol combined with a protein to form the light- absorbing molecule bacteriorhodopsin, and make ATP using a chemiosmotic mechanism.

70. Figure 27.20 Extreme Halophiles

71. The Archaea
Thermoplasma is thermophilic and acidophilic; it has no cell wall, an aerobic metabolism, and lives in coal deposits.
It has the smallest genome (1,100,000 base pairs) of the archaea.