Week 8 Discussion.pdf - Week 8 Discussion 1 Paper#2...

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Unformatted text preview: Week 8 Discussion 1. Paper #2 Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms 3 “ What questions were addressed in the paper? 4 Purpose Are electrically conductive appendages exclusive to dissimilatory metal-reducing bacteria? What is the function of nanowires in bacteria that are not metal-reducing? Under what conditions can they use nanowires? 5 Some definitions ▫ Nanowires: electrically conductive pilus-like appendages in direct response to electron-acceptor limitation ▫ Dissimilatory reduction of metals: globally important biogeochemical process driving the cycling of Fe and Mn in order to solubilize metals for use in their electron transport system 6 “ What were the main conclusions from the paper? Importance? 7 Conclusions ▫ ▫ ▫ ▫ S. oneidensis produces electrically conductive nanowires in response to oxygen limitation ▪ This different electron transfer method helps us understand the mechanism in dissimilatory metal-reducing bacteria S. oneidensis can reduce silica ferrihydrite to magnetite nanoparticles by bacterial nanowires ▪ Nanowires might facilitate far-field transport of electrons from cells to solid phases located at significant distances from the bacteria MtrC, OmcA, and GspD are involved in electron transport by nanowires The photosynthetic cyanobacterium Synechocystis and the thermophilic fermentative bacterium Pelotomaculum thermopropionicum also produce nanowires 8 “ What experiments were performed to answer these questions? 9 Experiments 1. Grow S. oneidensis wild type strains in continuous culture with electron-acceptor limitation and low agitation and use SEM and epifluorscence micrograph for imaging 2. Transmission EM analyses to determine extracellular reduction of silica ferrihydrite to magnetite nanoparticles 3. Create mutants without functioning mtrC and omcA genes. Also create mutants without GspD. Use SEM analysis to determine whether nanowires were produced 4. STM and tunneling spectroscopy to determine whether other strains produce nanowires 10 “ For each experiment, what conclusion did the experiment allow? What were the caveats of each experiment? What experiments ruled out these alternatives? 11 Conclusions from experiments 1. 2. 3. 4. Extracellular appendages are created under oxygen-limited growth conditions in S. oneidensis cultures and they are electrically conductive because the graphite in the plate was highly ordered. S. oneidensis can reduce silica ferrihydrite to magnetite. Because the cells were in anaerobic conditions and silica ferrihydrite was the only terminal electron acceptor, the strain must have used iron reduction to digest the lactate in the medium MtrC, OmcA, and GspD are involved in electron transport by nanowires. By knocking these out, there was less production of nanowires in the mutants than in the wild-type. Nanowires are also produced in Synechocystis and P. thermopropionicum. 2. Lecture 12 Metabolic Diversity II 13 Syntrophy ▫ ▫ ▫ ▫ “Eating together” Microbes constantly interact with other populations, so many have coevolved to optimize their trophic strategies Primarily in anoxic environments where there aren’t as many nutrients available Example: one organism is fermenting and can use ethanol as electron donor and releases hydrogen gas (not favorable) ▪ H2 shunted to be used in methanogenesis in another organism (favorable) ▪ Hydrogen is electron donor ▪ Overall is favorable 14 Anoxic Decomposition How complex polymer is further reduced into methane and carbon dioxide 1. 2. 3. 4. Cellulolytic bacteria break down cellulose into monomers (glucose) through hydrolysis Fermentative organisms can break down glucose and ferment it into hydrogen and carbon dioxide Produce acetate through acetogenesis in homoacetogens Use syntrophy with methanogens to get methane and carbon dioxide Like signal transduction cascades, the chemistry and biology of natural environments are controlled by trophic cascades 15 Phototrophy Energy: use light as energy source Photoautotrophs Photoheterotrophs Carbon: Carbon dioxide Carbon: organic carbon Photosynthesis: use CO2 and reducing it to organic sugars to create O2 A facultative nutritional mode: mixotrophic (can grow photosynthetically and fix CO2, but some can use sugars when available H2S, So, H2, and H2O are electron donors Examples: ▫ ▫ ▫ ▫ Green non-sulfur (Chloroflexus) Purple non-sulfur (Rhodospirillum) Halophiles - bacteriorhodopsins ▪ Grow in salt; bacteriorhodopsins can absorb light and pump protons Marine bacteria- proteorhodopsins 16 Photosynthesis: photolithoautotrophy Oxygenic photosynthesis ▫ ▫ ▫ ▫ ▫ ▫ ▫ ▫ ▫ Reducing power: H2O to ½ O2 Carbon source: CO2 to (CH2O)n Energy: ATP Plants, algae, cyanobacteria, H2O is electron donor ▪ Oxygenic means water is electron donor Contain chlorophyll 2 photosystems (“Z-scheme”) Non-cyclic phosphorylation Light required for reducing power (NADH) and energy conservation Anoxygenic photosynthesis ▫ ▫ ▫ ▫ ▫ ▫ ▫ ▫ Electron donor is H2S→ S0 → SO42▪ Also H2 and Fe2+ Caron source: CO2 → sugars Light is not required to get electrons Light is required to create proton motive force to generate ATP Purple, green sulfur, green nonsulfur bacteria and heliobacteria Contain bacteriochlorophyll One photosystem Cyclic photophosphorylation 17 Light Harvesting Pigments Pyrophin ring (like cytochromes) Long fatty-acyl phytol chains to anchor membrane The chemical diversity of chlorophyll molecules alters the absorption spectrum for light harvesting Chlorophyll a ▫ ▫ Oxygenic phototrophs Chlorophyll a is the principal molecule in green plants, algae, and cyanobacteria Bacteriochlorophyll a ▫ ▫ ▫ Anoxygenic phototrophs Extensive chemical diversity Distinguished based on different R groups 18 Absorption Spectra Chlorophyll A ▫ ▫ Chlorophyll A absorbs predominantly indigo/violet range and at the yellow-orange length Doesn’t absorb green--why plants and cyanobacteria are green Bacteriochlorophyll A ▫ ▫ ▫ Bacteriochlorophyll appear reddish purple because they do not absorb that light Absorb mostly UV light (high energy light) Also absorb infrared light (heat) 19 Accessory Pigments Carotenoids ▫ ▫ ▫ ▫ ▫ ▫ Carotenes and xanthophylls Function in photoprotection Prevent oxidative damage Isoprenoid chains Absorb blue light predominantly Prevent damage from excessive UV exposure by absorbing UV light Phycobiliproteins ▫ ▫ ▫ ▫ ▫ Antennae pigments: phycobilisomes that absorb additional quantities of light to help funnel light energy Found in cyanobacteria 3 primary pigment types Phycobilisome content increases when light intensity decreases Appear as blue-green algae These accessory pigments are intimately associated with the light harvesting complexes and increase light capture efficiency 20 Photosynthetic Membranes ▫ ▫ ▫ ▫ ▫ Bacteria do not have chloroplasts Photosynthetic reaction centers are integrated into internal membrane systems Thylakoid membranes (cyanobacteria) --oxygenic ▪ Internal membrane systems that have lots of chlorophyll to maximize light energy absorption Cytoplasmic membrane invaginations (purple bacteria) ▪ Creates additional surface area to optimize energy production Chlorosomes (green bacteria) ▪ Additional membrane systems; chlorophyll run lengthwise across cell 21 Anoxygenic photosynthesis ▫ ▫ ▫ ▫ ▫ ▫ Purple, green sulfur, green nonsulfur bacteria, and heliobacteria Can use external electron donors (H2S, S2O32-, S0, Fe2+) Poor electron donor (P870) is converted to a strong electron donor (P870*) through light activation ▪ Electrons can now flow down redox tower to quinone pool to set up PMF to get NADPH Cyclic photophosphorylation (no terminal electron acceptor) ▪ Highly efficient because same electron is coupled with ATP synthesis Light energy responsible for generation of PMF (ATP synthesis) but not reducing power Problem is that once electron is in quinone pool, hard to get back up redox power to get NADP+ ▪ Need to burn ATP to generate NADPH or use external electron donors 3. Lecture 13 Microbial Ecology I 23 Oxygenic Photosynthesis ▫ ▫ ▫ ▫ ▫ ▫ ▫ 2 photosystems Photosystem II has a high E0’ value Electrons from H2O (single electron donor) generate proton motive force and NADPH reducing power Photosystem I responsible for NADPH synthesis (required for anabolic synthesis) When NADPH levels are good, cyclic electron flow can produce more ATP -- separate from creating reducing equivalents Chlorophyll a is in Photosystems I and II Phycobilisomes are in Photosystem II 24 Autotrophy ▫ ▫ ▫ ▫ ▫ ▫ Multiple pathways for CO2 fixation Calvin-Benson cycle: CO2 from atmosphere is incorporated into sugars Cyanobacteria, green plants, algae, purple bacteria, chemolithotrophs, and archaea RuBisCO: required for Calvin-Benson cycle; most important enzyme in the world; found across the tree of life Light provides the energy and CO2 is the substrate for building macromolecules ▪ A lot of ATP and NADPH required Some species conentrate RubisCO inside their cells as inclusion bodies (“carboxysomes”) 25 Autotrophy Autotrophic CO2 fixation pathways ▫ ▫ ▫ ▫ ▫ Calvin cycle ▪ Cyanobacteria, proteobacteria, plants and algae Reductive citric acid cycle ▪ Proteobacteria, green sulfur bacteria, aquifex/hydrogenobacter, crenarchaeota (archaea) Reductive acetyl-CoA pathway ▪ Strictly anaerobic gram-positive bacteria and proteobacteria 3-hydroxypropionate/malyl-CoA cycle ▪ Green nonsulfur bacteria Novel 3-hydroxypropionate/4-hydroxybutyrate cycle ▪ Archaea 26 Chemolithotrophy ▫ ▫ ▫ ▫ ▫ ▫ ▫ Energy and electrons from the oxidation of inorganic compounds Chemolithoautotrophs source of carbon is CO2 Chemolithoheterotrophs source of carbon is organics ▪ Majority of carbon and energy from organic compounds but can supplement diet with inorganic reactions Inorganic donor sources are diverse ▪ Chemolithotrophs eat inorganic compounds that are highly abundant (lots of food!) Electron acceptors are also diverse ▪ Aerobic conditions = O2 ▪ Anaerobic conditions = NO3, SO4, metals, organics, etc. Energy production proceeds via PMF and ATPases Reducing power comes directly from inorganic donor or reverse electron flow 27 Diversity of Chemolithotrophs ▫ ▫ ▫ Inorganic electron donors: H2, H2S, So, NH4, NO2-, Fe2+, etc. Electron acceptors: O2 , SO42- , NO3 - , metals, organics, etc. Example: Beggiatoa ▪ H2S → SO42▪ O2 is the electron acceptor 28 Oxidation of Reduced Sulfur Compounds ▫ ▫ ▫ Electrons from sulfur oxidation feed into electron transport chain ▪ More energy from more reduced forms Reverse electron flow necessary for NAD(P)H production because e - donors are more positive than NAD+ ▪ Spend some ATP CO2 fixation proceeds via Calvin Benson cycle or reverse TCA 29 Oxidation of Reduced Sulfur Compounds 1. 2. 3. 4. Electrons come in and go to quinone pool Generate proton motive force Go back through and generate NAD+ to NADH Use hydrogen sulfide electrons that fall and couple them with oxygen as terminal electron acceptor 5. ATP generated 30 Iron Oxidation ▫ ▫ ▫ ▫ ▫ ▫ Fe2+ (ferrous) → Fe3+ (ferric) Ferrous iron spontaneously oxidizes to ferric under oxic conditions (at pH 7) but is stable at low pH (pH < 3) -- rust ▪ Most iron bacteria are acidophilic (like low pH) Use external electron donation Need reverse electron flow to get NADH back Lots of protons on the outside so proton gradient is large, but can’t take in protons because making inside too acidic is lethal Cells must oxidize a lot of Fe2+ to get energy at low pH (very short electron transport chain because very close to oxygen) ...
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