1. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Brock Biology of Microorganisms Twelfth Edition Madigan / Martinko Dunlap / Clark Metabolic Diversity: Phototrophy, Autotrophy, Chemolithotrophy, and Nitrogen Fixation Chapter 20 Lectures by Buchan & LeCleir

2. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings I. The Phototrophic Way of Life  20.1 Photosynthesis  20.2 Chlorophylls and Bacteriochlorophylls  20.3 Carotenoids and Phycobilins  20.4 Anoxygenic Photosynthesis  20.5 Oxygenic Photosynthesis

3. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.1 Photosynthesis  Photosynthesis is the most important biological process on Earth  Phototrophs are organisms that carry out photosynthesis  Most phototrophs are also autotrophs  Photosynthesis requires light-sensitive pigments called chlorophyll  Photoautotrophy requires ATP production and CO 2 reduction  Oxidation of H 2 O produces O 2 (oxygenic photosynthesis)  Oxygen not produced (anoxygenic photosynsthesis)

4. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.1 Classification of Phototrophic Organisms

5. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.2 Patterns of Photosynthesis

6. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.2 Patterns of Photosynthesis

7. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.2 Chlorophylls and Bacteriochlorophylls  Organisms must produce some form of chlorophyll (or bacteriochlorophyll) to be photosynthetic  Chlorophyll is a porphyrin  Number of different types of chlorophyll exist  Different chlorophylls have different absorption spectra  Chlorophyll pigments are located within special membranes  In eukaryotes, called thylakoids  In prokaryotes, pigments are integrated into cytoplasmic membrane

8. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.3a Structure and Spectra of Chloro- and Bacteriochlorophyll

9. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.3b Structure and Spectra of Chloro- and Bacteriochlorophyll Absorption Spectrum

10. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.4 Structure of All Known Bacteriochlorophylls

11. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.4 Structure of All Known Bacteriochlorophylls

12. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.4 Structure of All Known Bacteriochlorophylls

13. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.5a Photomicrograph of Algal Cell Showing Chloroplasts

14. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.5b Chloroplast Structure

15. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.2 Chlorophylls and Bacteriochlorophylls  Reaction centers participate directly in the conversion of light energy to ATP  Antenna pigments funnel light energy to reaction centers  Chlorosomes function as massive antenna complexes  Found in green sulfur bacteria

16. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.6 Arrangement of Light-Harvesting Chlorophylls

17. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.7 The Chlorosome of Green Sulfur and Nonsulfur Bacteria Electron Micrograph of Cell of Green Sulfur Bacterium

18. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.7 The Chlorosome of Green Sulfur and Nonsulfur Bacteria Model of Chromosome Structure

19. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.3 Carotenoids and Phycobilins  Phototrophic organisms have accessory pigments in addition to chlorophyll, including carotenoids and phycobiliproteins  Carotenoids  Always found in phototrophic organisms  Typically yellow, red, brown, or green  Energy absorbed by carotenoids can be transferred to a reaction center  Prevent photo-oxidative damage to cells

20. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.8 Structure of  -carotene, a Typical Carotenoid

21. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.9 Structures of Some Common Carotenoids

22. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.9 Structures of Some Common Carotenoids

23. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.3 Carotenoids and Phycobilins  Phycobiliproteins are main antenna pigments of cyanobacteria and red algae  Form into aggregates within the cell called phycobilisomes  Allow cell to capture more light energy than chlorophyll alone

24. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.10 Phycobiliproteins and Phycobilisomes

25. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.11 Absorption Spectrum with an Accessory Pigment

26. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.4 Anoxygenic Photosynthesis  Anoxygenic photosynthesis is found in at least four phyla of Bacteria  Electron transport reactions occur in the reaction center of anoxygenic phototrophs  Reducing power for CO 2 fixation comes from reductants present in the environment (i.e., H 2 S, Fe 2+, or NO 2- )  Requires reverse electron transport for NADH production in purple phototrophs

27. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.12 Membranes in Anoxygenic Phototrophs Chromatophores Lamellar Membranes in the Purple Bacterium Ectothiorhodospira

28. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.13 Structure of Reaction Center in Purple Bacteria Arrangement of Pigment Molecules in Reaction Center

29. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.13 Structure of Reaction Center in Purple Bacteria Molecular Model of the Protein Structure of the Reaction Center

30. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.14 Example of Electron Flow in Anoxygenic Photosynthesis

31. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.15 Arrangement of Protein Complexes in Reaction Center

32. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.16 Map of Photosynthetic Gene Cluster in Purple Phototroph

33. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.17 Phototrophic Purple and Green Sulfur Bacteria Purple Bacterium, Chromatium okenii Green Bacterium, Chlorobium limicola

34. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.18 Electron Flow in Purple, Green, Sulfur and Heliobacteria

35. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.5 Oxygenic Photosynthesis  Oxygenic phototrophs use light to generate ATP and NADPH  The two light reactions are called photosystem I and photosystem II  “Z scheme” of photosynthesis  Photosystem II transfers energy to photosystem I  ATP can also be produced by cyclic photophosphorylation

36. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.19 The “Z scheme” in Oxygenic Photosynthesis

37. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings II. Autotrophy  20.6 The Calvin Cycle  20.7 Other Autotrophic Pathways in Phototrophs

38. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.6 The Calvin Cycle  The Calvin Cycle  Named for its discoverer Melvin Calvin  Fixes CO 2 into cellular material for autotrophic growth  Requires NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase  6 molecules of CO 2 are required to make 1 molecule of glucose

39. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.21a Key Reactions of the Calvin Cycle

40. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.21b Key Reactions of the Calvin Cycle

41. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.21c Key Reactions of the Calvin Cycle

42. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.22 The Calvin Cycle

43. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.7 Other Autotrophic Pathways in Phototrophs  Green sulfur bacteria use the reverse citric acid cycle to fix CO 2  Green nonsulfur bacteria use the hydroxyproprionate pathway to fix CO 2

44. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.24a Autotrophic Pathways in Phototrophic Green Bacteria

45. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.24b Autotrophic Pathways in Phototrophic Green Bacteria

46. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings III. Chemolithotrophy  20.8 The Energetics of Chemolithotrophy  20.9 Hydrogen Oxidation  20.10 Oxidation of Reduced Sulfur Compounds  20.11 Iron Oxidation  20.12 Nitrification  20.13 Anammox

47. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.8 The Energetics of Chemolithotrophy  Chemolithotrophs are organisms that obtain energy from the oxidation of inorganic compounds  Mixotrophs are chemolithotrophs that require organic carbon as a carbon source  Many sources of reduced molecules exist in the environment  The oxidation of different reduced compounds yields varying amounts of energy

48. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Energy Yields from Oxidation of Inorganic Electron Donors

49. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.9 Hydrogen Oxidation  Anaerobic H 2 oxidizing Bacteria and Archaea are known  Catalyzed by hydrogenase  In the presence of organic compounds such as glucose, synthesis of Calvin cycle and hydrogenase enzymes is repressed

50. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.25 Two Hydrogenases of Aerobic H 2 Bacteria

51. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.10 Oxidation of Reduced Sulfur Compounds  Many reduced sulfur compounds are used as electron donors  Discovered by Sergei Winogradsky  H 2 S, S 0, S 2 O 3 - are commonly used  One product of sulfur oxidation is H +, which results in a lowering of the pH of its surroundings  Sox system oxidizes reduced sulfur compounds directly to sulfate  Usually aerobic, but some organisms can use nitrate as an electron acceptor

52. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.26 Sulfur Bacteria

53. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.27a Oxidation of Reduced Sulfur Compounds Steps in the Oxidation of Different Compounds

54. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.27b Oxidation of Reduced Sulfur Compounds

55. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.11 Iron Oxidation  Ferrous iron (Fe 2+ ) oxidized to ferric iron (Fe 3+ )  Ferric hydroxide precipitates in water  Many Fe oxidizers can grow at pH <1  Often associated with acidic pollution from coal mining activities  Some anoxygenic phototrophs can oxidize Fe 2+ anaerobically using Fe 2+ as an electron donor for CO 2 reduction

56. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.28 Iron-Oxidizing Bacteria Acid Mine Drainage

57. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.28 Iron-Oxidizing Bacteria Cultures of A. Ferrooxidans Shown in Dillution Series

58. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.29 Iron Bacteria Growing at Neutral pH: Sphaerotilus

59. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.30 Electron Flow During Fe 2+ Oxidation

60. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Fe 2+ Oxidation in Anoxic Tube Cultures Figure 20.31 Ferrous Iron Oxidation by Anoxygenic Phototrophs

61. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.31 Ferrous Iron Oxidation by Anoxygenic Phototrophs Phase-contrast Photomicrograph Of an Iron-Oxidizing Purple Bacterium

62. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.12 Nitrification  NH 3 and NO 2 - are oxidized by nitrifying bacteria during the process of nitrification  Two groups of bacteria work in concert to fully oxidize ammonia to nitrate  Key enzymes are ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase  Only small energy yields from this reaction  Growth of nitrifying bacteria is very slow

63. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.32 Oxidation of Ammonia by Ammonia-Oxidizing Bacteria

64. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.33 Oxidation of Nitrite to Nitrate by Nitrifying Bacteria

65. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.13 Anammox  Anammox: anoxic ammonia oxidation  Performed by unusual group of obligate aerobes  Anammoxosome is compartment where anammox reactions occur  Protects cell from reactions occuring during anammox  Hydrazine is an intermediate of anammox  Anammox is very beneficial in the treatment of sewage and wastewater

66. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.34a-b Anammox Phase-contrast Photomicrograph of Brocadia Anammoxidans cells Transmission Electronic Micrograph of a Cell

67. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.34c Reactions in the Anammoxosome

68. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings IV. Nitrogen Fixation  20.14 Nitrogenase and Nitrogen Fixation  20.15 Genetics and Regulation of Nitrogen Fixation

69. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.14 Nitrogenase and Nitrogen Fixation  Only certain prokaryotes can fix nitrogen  Some nitrogen fixers are free living and others are symbiotic  Reaction is catalyzed by nitrogenase  Sensitive to the presence of oxygen  A wide variety of nitrogenases use different metal cofactors  Nitrogenase activity can be assayed using the acetylene reduction assay

70. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.35 FeMo-co, the Iron-Molybdenum Cofactor from Nitrogenase

71. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.36 Nitrogenase Function

72. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.37 Induction of Slime Formation by O 2 in Nitrogen-Fixing Cells

73. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.38 Reaction of Nitrogen Fixation in S. thermoautotrophicus

74. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.39 The Acetylene Reduction Assay for Nitrogenase Activity

75. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.15 Genetics and Regulation of Nitrogen Fixation  Highly regulated process because it is such an energy- demanding process  nif regulon coordinates regulation of genes essential to nitrogen fixation  Oxygen and ammonia are the two main regulatory effectors

76. Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.40 The nif regulon in K. pneumoniae