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Brock Biology of Microorganisms Twelfth Edition Madigan / Martinko Chapter 20 Dunlap / Clark Metabolic Diversity: Phototrophy, Autotrophy, Chemolithotrophy, and Nitrogen Fixation Lectures by Buchan & LeCleir 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 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 CO2 reduction Oxidation of H2O produces O2 (oxygenic photosynthesis) Oxygen not produced (anoxygenic photosynsthesis) Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Classification of Phototrophic Organisms Figure 20.1 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Patterns of Photosynthesis Figure 20.2 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Patterns of Photosynthesis Figure 20.2 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure and Spectra of Chloro- and Bacteriochlorophyll Figure 20.3a Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure and Spectra of Chloro- and Bacteriochlorophyll Absorption Spectrum Figure 20.3b Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of All Known Bacteriochlorophylls Figure 20.4 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of All Known Bacteriochlorophylls Figure 20.4 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of All Known Bacteriochlorophylls Figure 20.4 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Photomicrograph of Algal Cell Showing Chloroplasts Figure 20.5a Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Chloroplast Structure Figure 20.5b 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Arrangement of Light-Harvesting Chlorophylls Figure 20.6 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The Chlorosome of Green Sulfur and Nonsulfur Bacteria Electron Micrograph of Cell of Green Sulfur Bacterium Figure 20.7 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The Chlorosome of Green Sulfur and Nonsulfur Bacteria Model of Chromosome Structure Figure 20.7 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of -carotene, a Typical Carotenoid Figure 20.8 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structures of Some Common Carotenoids Figure 20.9 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structures of Some Common Carotenoids Figure 20.9 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Phycobiliproteins and Phycobilisomes Figure 20.10 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Absorption Spectrum with an Accessory Pigment Figure 20.11 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 CO2 fixation comes from reductants present in the environment (i.e., H2S, Fe2+, or NO2-) Requires reverse electron transport for NADH production in purple phototrophs Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Membranes in Anoxygenic Phototrophs Chromatophores Lamellar Membranes in the Purple Bacterium Ectothiorhodospira Figure 20.12 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of Reaction Center in Purple Bacteria Arrangement of Pigment Molecules in Reaction Center Figure 20.13 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Structure of Reaction Center in Purple Bacteria Molecular Model of the Protein Structure of the Reaction Center Figure 20.13 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Example of Electron Flow in Anoxygenic Photosynthesis Figure 20.14 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Arrangement of Protein Complexes in Reaction Center Figure 20.15 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Map of Photosynthetic Gene Cluster in Purple Phototroph Figure 20.16 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Phototrophic Purple and Green Sulfur Bacteria Purple Bacterium, Chromatium okenii Green Bacterium, Chlorobium limicola Figure 20.17 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Electron Flow in Purple, Green, Sulfur and Heliobacteria Figure 20.18 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The “Z scheme” in Oxygenic Photosynthesis Figure 20.19 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings II. Autotrophy 20.6 The Calvin Cycle 20.7 Other Autotrophic Pathways in Phototrophs 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 CO2 into cellular material for autotrophic growth Requires NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase 6 molecules of CO2 are required to make 1 molecule of glucose Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Key Reactions of the Calvin Cycle Figure 20.21a Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Key Reactions of the Calvin Cycle Figure 20.21b Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Key Reactions of the Calvin Cycle Figure 20.21c Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The Calvin Cycle Figure 20.22 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 CO2 Green nonsulfur bacteria use the hydroxyproprionate pathway to fix CO2 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Autotrophic Pathways in Phototrophic Green Bacteria Figure 20.24a Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Autotrophic Pathways in Phototrophic Green Bacteria Figure 20.24b 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 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Energy Yields from Oxidation of Inorganic Electron Donors Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.9 Hydrogen Oxidation Anaerobic H2 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Two Hydrogenases of Aerobic H2 Bacteria Figure 20.25 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 H2S, S0, S2O3- 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Sulfur Bacteria Figure 20.26 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Oxidation of Reduced Sulfur Compounds Steps in the Oxidation of Different Compounds Figure 20.27a Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Oxidation of Reduced Sulfur Compounds Figure 20.27b Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings 20.11 Iron Oxidation Ferrous iron (Fe2+) oxidized to ferric iron (Fe3+) 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 Fe2+ anaerobically using Fe2+ as an electron donor for CO2 reduction Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Iron-Oxidizing Bacteria Acid Mine Drainage Figure 20.28 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Iron-Oxidizing Bacteria Cultures of A. Ferrooxidans Shown in Dillution Series Figure 20.28 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Iron Bacteria Growing at Neutral pH: Sphaerotilus Figure 20.29 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Electron Flow During Fe2+ Oxidation Figure 20.30 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Ferrous Iron Oxidation by Anoxygenic Phototrophs Fe2+ Oxidation in Anoxic Tube Cultures Figure 20.31 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Ferrous Iron Oxidation by Anoxygenic Phototrophs Phase-contrast Photomicrograph Of an Iron-Oxidizing Purple Bacterium Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Figure 20.31 20.12 Nitrification NH3 and NO2- 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Oxidation of Ammonia by Ammonia-Oxidizing Bacteria Figure 20.32 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Oxidation of Nitrite to Nitrate by Nitrifying Bacteria Figure 20.33 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Anammox Phase-contrast Photomicrograph of Brocadia Anammoxidans cells Transmission Electronic Micrograph of a Cell Figure 20.34a-b Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Reactions in the Anammoxosome Figure 20.34c 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 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 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings FeMo-co, the Iron-Molybdenum Cofactor from Nitrogenase Figure 20.35 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Nitrogenase Function Figure 20.36 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Induction of Slime Formation by O2 in Nitrogen-Fixing Cells Figure 20.37 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings Reaction of Nitrogen Fixation in S. thermoautotrophicus Figure 20.38 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The Acetylene Reduction Assay for Nitrogenase Activity Figure 20.39 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 energydemanding process nif regulon coordinates regulation of genes essential to nitrogen fixation Oxygen and ammonia are the two main regulatory effectors Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings The nif regulon in K. pneumoniae Figure 20.40 Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings