Bacteria, Archaea, and Viruses

1. 19 Bacteria, Archaea, and Viruses

2. Chapter 19 Bacteria, Archaea, and Viruses • Key Concepts • 19.1 Life Consists of Three Domains That Share a Common Ancestor • 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life • 19.3 Ecological Communities Depend on Prokaryotes • 19.4 Viruses Have Evolved Many Times

3. Chapter 19 Opening Question How do Vibrio populations detect when they are dense enough to produce bioluminescence?

4. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor • All organisms have: • Plasma membranes and ribosomes • Metabolic pathways (e.g., glycolysis) • Conservative DNA replication • DNA that encodes proteins • Shared features indicate that all life is related, but major differences have also evolved.

5. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Three domains of life: Bacteria—prokaryotes Archaea—prokaryotes Eukarya—eukaryotes

6. Figure 19.1 The Three Domains of the Living World

7. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Prokaryotes differ from eukaryotes. All are unicellular Divide by binary fission, not mitosis DNA is often circular, not in a nucleus No membrane-enclosed organelles

8. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Genetic studies show that the three domains had a single common ancestor. Some eukaryote genes are most closely related to those of archaea, while others are most closely related to those of bacteria. Mitochondria and chloroplasts of eukaryotes originated through endosymbiosis with a bacterium.

9. Table 19.1 The Three Domains of Life on Earth

10. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Study of prokaryotes was not possible until microscopes were developed. Before DNA sequencing, classification was based on phenotypic characters such as shape, color, motility, nutrition, and cell wall structure.

11. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Most bacteria cell walls contain peptidoglycan, which is unique to bacteria. Antibiotics target peptidoglycan because eukaryote cells don’t have it, thus there is no harm to human cells.

12. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Bacteria can be grouped by the Gram stain response, which is based on differences in cell wall structure: Gram-positive bacteria appear blue to purple. Gram-negative bacteria appear pink to red.

13. Figure 19.2 The Gram Stain and the Bacterial Cell Wall (Part 1)

14. Figure 19.2 The Gram Stain and the Bacterial Cell Wall (Part 2)

15. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Common bacteria cell shapes: Sphere—coccus (plural cocci), occur singly or in plates, blocks, or clusters Rod—bacillus (plural bacilli) Spiral or helical—helix (plural helices) Rods and helical shapes may form chains or clusters. Other bacterial shapes form filaments and branched filaments.

16. Figure 19.3 Bacterial Cell Shapes

17. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Sequencing of ribosomal RNA (rRNA) genes is useful for phylogenetic studies because: rRNA was present in the common ancestor of all life. • All free-living organisms have rRNA. • Lateral transfer of rRNA genes among distantly related species is unlikely. • rRNA has evolved slowly.

18. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Whole genome sequencing has revealed that even distantly related prokaryotes sometimes exchange genetic material. Transformation, conjugation, and transduction allow exchange of genetic information between prokaryotes without reproduction. In lateral gene transfer, genes move “sideways” from one species to another. When sequenced, gene trees will not match the organismal tree.

19. Figure 19.4 Lateral Gene Transfer Complicates Phylogenetic Relationships

20. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Genes that result in new adaptations that confer higher fitness are most likely to be transferred. Genes for antibiotic resistance are often transferred among bacterial species.

21. Concept 19.1 Life Consists of Three DomainsThat Share a Common Ancestor Many prokaryote species, and perhaps whole clades, have not been described by biologists. Many have resisted efforts to grow them in pure culture. Biologists now examine gene sequences collected from random samples of the environment. Many new sequences imply there are thousands more prokaryotic species.

22. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Prokaryotes are the most successful organisms on Earth in terms of number of individuals. The number of prokaryotes in the ocean is perhaps 100 million times as great as the number of stars in the visible universe. They are found in every type of habitat on Earth. We will describe eight bacterial groups.

23. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Low-GC Gram-positives (Firmicutes) Low ratio of G-C to A-T base pairs in DNA. Some are gram-negative, and some have no cell wall. Some produce heat-resistant endospores that can survive unfavorable conditions. Some can survive for 1,000 years. Includes Clostridium and Bacillus.

24. Figure 19.5 A Structure for Waiting Out Bad Times

25. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Bacillus anthracis produces an exotoxin that causes anthrax. The endospores have been used as a bioterrorism agent. Staphylococcus (staphylococci) are abundant on skin and cause boils and other skin problems. S. aureus can also cause respiratory, intestinal, and wound infections.

26. Figure 19.6 Staphylococci

27. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Mycoplasmas have no cell wall, are extremely small, and have a very small genome. They have less than half as much DNA as other prokaryotes, which may represent the minimum amount of DNA needed for a living cell.

28. Figure 19.7 Tiny Cells

29. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life High-GC Gram-positives (Actinobacteria) Higher ratio of G-C to A-T base pairs. Branched filaments; some form reproductive spores at filament tips. Most antibiotics are from this group. Mycobacterium tuberculosis causes tuberculosis; oldest know human pathogen.

30. Figure 19.8 Actinomycetes Are High-GC Gram-Positives

31. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Hyperthermophilic bacteria Live at extreme high temperatures (extremophiles)—hot springs, volcanic vents, underground oil reservoirs. High temperatures may have been the ancestral condition on Earth when prokaryotes evolved. Monophyly of this group is not well established.

32. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Hadobacteria Also extreme thermophiles. Deinococcus survive cold as well as hot temperatures and are resistant to radiation. They can consume nuclear waste. Thermus aquaticus was isolated from a hot spring; source of the thermally stable DNA polymerase used in PCR.

33. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Cyanobacteria Photosynthetic; have blue-green pigments. Many species fix nitrogen. Chloroplasts of eukaryotes are derived from an endosymbiotic cyanobacterium. Some colonies differentiate into vegetative cells, spores, and heterocysts specialized for N-fixation.

34. Figure 19.9 Cyanobacteria (Part 1)

35. Figure 19.9 Cyanobacteria (Part 2)

36. Figure 19.9 Cyanobacteria (Part 3)

37. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Spirochetes Gram-negative; motile Unique axial filaments (modified flagella) that rotate Many are human parasites, some are pathogens (syphilis, Lyme disease), others are free living.

38. Figure 19.10 Spirochetes Get Their Shape from Axial Filaments (Part 1)

39. Figure 19.10 Spirochetes Get Their Shape from Axial Filaments (Part 2)

40. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Chlamydias Can live only as parasites in cells of other organisms. Gram-negative; extremely small Can take up ATP from host cell with translocase Complex life cycle with two forms—elementary bodies and reticulate bodies

41. Figure 19.11 Chlamydias Change Form during Their Life Cycle

42. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Proteobacteria: largest group of bacteria Mitochondria of eukaryotes were derived from a proteobacterium by endosymbiosis. Some are photoautotrophs that use light energy to metabolize sulfur; some are N-fixers (Rhizobium). Escherichia coli is one of the most studied organisms on Earth.

43. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Agrobacterium tumefaciens causes crown gall disease of plants and has a plasmid used in recombinant DNA studies. The proteobacteria include many pathogens— cholera, bubonic plague, salmonella.

44. Figure 19.12 Proteobacteria Include Human Pathogens

45. Figure 19.13 Crown Gall

46. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Separation of the Archaea domain from bacteria and eukaryotes is based on genome sequencing. Many archaea live in extreme habitats—high temperatures, low oxygen, high salinity, extreme pH. Many others are common in soil and in the oceans.

47. Figure 19.14 What Is the Highest Temperature Compatible with Life? (Part 1)

48. Figure 19.14 What Is the Highest Temperature Compatible with Life? (Part 2)

49. Concept 19.2 Prokaryote Diversity Reflects the Ancient Origins of Life Archaea are divided into two main groups, Euryarcheota and Crenarcheota Two recently discovered groups: Korarchaeota (known only from DNA in hot springs) Nanoarchaeota, a parasite on cells of a crenarchaeote in deep sea hydrothermal vents All lack peptidoglycan in the cell walls and have unique lipids in the cell membranes.

50. Figure 19.18 A Nanoarchaeote Growing in Mixed Culture with a Crenarchaeote