Microbio Lecture 15 - 10-29-09.docx

Lecture 14 Continue Lecture 15 ? Groups of Microorganisms and Metabolic Diversity Groups of microorganism Phylogeny of the Bacteria based on 16S rRNA sequences ? Figure 15.1 Phylum XII Proteobacteria Largest Group of Bacteria: Very Diverse in morphology and metabolic pathways 5 different subdivisions: alpha, beta, gamma Includes members that are: Phototrohphic Chemolithotrophic Heterotrophic Proteobacteria inclues membera that are cocci, straight rods, curved rods, budding and appendaged cells, filamentous forms and spirilla Enteric bacteria ? In Gamma subdivision Gram negative; if notile ? peritrichous flagella; group includes pathogens E. coli ? intestinal inhabitant; some strains pathogenic Salmonella typhi ? enteric pathogen Shingella dysenteriae Enteric pathogen ? non-motile: closely related to E. coli Erwinina carotovora Plant pathogen In Beta subdivision: Gram negative, spiral shaped, polar flagella Spirillum volutans ? freshwater microaerophile Bdellovibrio ? GOING TO BEO N THE EXAM!! Predator of other gram negative bacteria Developmental Cycle of Bdellevibro Bacteriovorus ? Figure 15.33b Release of progeny Attachment Penetration into prey periplasmic space Elongation of Bdellovibrio inside the bdelloplast ? consuming host nutrients Prey lysis ? the release of progeny Gram positives: ie ? Staphylococcus aureus, Lactobacillus acidophilus Endospore formers Bacillus subtilus ? aerobic rods Clostridium ? anaerobic rods Heliobacterium ? anaerobic photosynthetic rods Sporosarcina ? aerobic cocci Cell Wall-less Mycoplasma ? figure 16.9 & 16.10 Mycoplasmas are phylogenetically related to gram positives even though they have no cell wall Have very small genomes and lack the enzyme to make peptidoglycan Membranes are stabilized by sterols and lipoglycans Often pathogenic and gain nutrients from their animal or plant hosts Phyla XIV: Actinobacteria Gram positives ? ex. Mycobacterium Acid fast bacteria Cell walls stabilized by unique lipid mycolic acid Often pathogens Actinomyces & Streptomyces: filamentous forms ? Figure 16.19, 16.20 & 16.23 Filamentous ? forms conidia Often produce antibiotics Phylum XVII ? Spriochetes Gram negative tightly coiled cells Unqiue method of motility ? no polar flagella Group contains free-living organisms and pathogens Examples ? Spriochaeta, Teponema, Borrelia Spriochaetes ? Figure 16.42 Endoglagellum (rigid, rotates, attached to one end of protoplasmic cylinder) Protoplastic cylinder and flagella rotate in opposite directions as the outer sheath Detailed phylogenetic Tree of the Archaea Archaea share many characteristics with both Bacteria and EUkarya Are spilit into two major groups Cenarchaeota mostly hyperthermophiles non-thermophilic marine organims Euryarchaeota Physiologically diverse Includes extreme halophiles and Extreme acidophiles Methanogens Autotrophy in Archaea proceed by multiple pathways: acetyl-CoA pathway, reductive citric acid cycle and 3-hydroxyproprionate cycle; some may have RubisCO enzymes Extremely Halophilic Archaea Halobacteria Extremely halophilic Archaea Have a requirement for hgiht salt concentrations Typically require at least 1.5M (~9%) NaCl for growth Found in solar salt evaporation ponds, salt lakes, and artificial saline habitats (ie. Saled foods) Halobacteria pump large amounts of K+ into the cell (exceeding the Na+ concentration ) to maintain water balance (compatible solute) Locations Great Salt lake, Utah Pigmented Haloalkaliphiles Growing in pH 10 Soda lake in Egypt Sea water Evaporation Ponds Near San Francisco Bay, Cali Halobacterium salinarum Light-driven synthesis of ATP in Halobacteria Certain halophiles are able to carry out light-mediated synthesis of ATP Utilizes the cytoplasmic membrane protein bacteriorhodopsin This protein contains retinal, a pigment that absorbs light energy and pumps a proton across the cell membrane ATP is synthesized using the proton translocation ATPase. Model for the Mechanism of Bacteriorhodopsin ? Figure 17.4 Retinal pigment is converted from the trans form to the cis form when it absorbs light at 570nm and translocates a proton across the membrane. The cis form then returns back to the trans isomer. Metabolic Diversity in Microorganisms Photosynthesis Photosynthesis is the conversion of light energy to chemical energy It occurs by absorption of quanta of light by chlorophyll (or bacteriochlorophyll) pigments It involves light harvesting and reaction center (RC) chlorophylls Photosystems contain membrane-bound electron transport systems Photosynthetic Bacteria ? Figure 20.1, and 20.2 Phototrophs ( used light as energy source) Photoautotrophs use CO2 Photoheterotrohphs use organic carbon Chlorophyllsa and bacteriochlorophyll a Red ? Rhodopseudomonas ? absorb at highest wave length ? as the wave length gets smaller the amount of energy collected has more energy Green ? Green alga Photsynthetic membranes Thylakoids in chloroplasts and cyanobacteria Rhodobacter ? chromatophors vesicles Green sulfur bacteria ? chlorosomes Proton Motor Force Light Harvesting complexes (antenna bacteriochlorophyll) funnel light to the reaction center. ? Figure 20.6 Reaction Center in purple bacteria (Type II RC) ? figure 20.13 Reaction center (RC) contains the L, M, and H polypeptides Special pair: bacteriochlorophylls (Bcl) Photopigments in RC:Special pair Bcl, assessor Bcl; 2 bacteriopheophytin Anoxygenic photosynthesis: model system - purple phototrophs (Rhodobacter). Reaction center donates e- to quinones (Type II reaction center). Figure 20.14 Photysnthetic membrane of purple phtorophic bacteria ? figure 20.15 Generation of PMF; ATP made by F1Fo ATPase Liquid Culture of Phototrophic Purple Bacteria Showing colors of stains contain various carotenoid pigments R. rubrum G-g ? strain contiang only bacteriochlorophyll a; no cartenoids Autrotrophy in Phototrophs In order for a cell to fix CO2, it must have a source of ATP and a source of reducing power in the form of NADH or NADPH To reduce NAD(P)+ to NAD(P)H the phototrophs? If the electron is used to reduce NAD(P)+, other sources of electrons must be used to re-reduce the oxidized reaction center In the purple sulfur bacteria (Chromatium), H2S or thiosulfate S2O3- can be used as electron donors Purple Non-sulfur bacteria can use organic compounds, H2 or (H2S at low concentrations as electron donors) Purple Sulfur Bacteria autorophs ? use reduced S compounds as electron donors for CO2 fixation Purple non-sulfur bacteria Some can grow in the dark as heterothrophs using organic compounds Most can also grow as autotrophs using H2 as an electron donor Some can use H2S as an electron donor if its levels are low Green Sulfur Bacteria ? figure 16.38 Photoautotrophs Chlorosomes Use H2S or So compounds as electron donor for CO2 fixation Heliobacteria ? Gram positive Photosynthesizing organism Bacteriochlorophyll g Green Sulfur Bacteri andheliobacteria have type I Reaction centers ? reduce an Fe-S center, then ferredoxin, which directly serves as e- donor for NAD(P)+ Purple S and purple Non sulfur bacteria have type Ii RC ? REVERSE ELCTRON TRANSPORT Electron Tower ? Thype RC reduces Fd which is very elctronengative so it can directly reduce NAD(P)+ Trpe II RC reduces quinine, which is more elctropostibe than NAD 0P)+ There fore energy must be consuedm in reverse? Co2 fixation ? calvin cycle ? Figure 20.21 Used by the purple bacteria 1,3 biphosphoglyceria acid to glyceraldehydes-3-phosphate Step that requires reducing power in the form of NAD(P)H Oxygenic Photosynthesis ? phylum X Cyanobacteria have phycobilins; proclorophytes have chlorophyll b These organism have both photosystem I and photosystem II Electron Flow ? oxygenic photosynthesis ? Figure 20.19 Photosystem ii chlorophyll 680nm absorbs light energy and ejects an e- P68o is so electropositive that it is immediately recued by water releasing O2 The electron form P860 passes through pheophytin, bound quinines and then to cytochrom bF and plastocyanin. The later donates e- to PSI. In this part of pathway PMF is generated, so ATP made General Microbiology                         Lecture 15 Groups of Microorganisms and Metabolic Diversity    Reading Assignments:  Bacterial Diversity 15.1, 15.2, 15.3, 15.4, 15.5, 15.11, 15.14, 16.1, 16.2, 16.3, 16.5, 16.6, 16.7, 16.8, 16.15,  16.16, 17.1, 17.2, 17.3.  Phototrophy, 20.1, 20.2, 20.4-20.7 (not genetics of photosynthesis), Chemolithotrophy 20.8-20.10.    In this section of the course, you are responsible for the names of the microorganisms that are discussed.  I. Overview of Phylogeny - based on 16S rRNA sequences:  selected Bacteria   a. Enteric Bacteria (part of Phylum Proteobacteria) - gram negative rods; if motile have peritrichous flagella; Escherichia, intestinal inhabitant; Salmonella &Shigella, enteric pathogens; some Erwinia are plant pathogens. b. Spirilla (part of the Phylum Proteobacteria) - gram negative, spiral-shaped with polar flagella. Genus Spirillum - often found as freshwater microaerophiles; GenusBdellovibrio - small predator bacteria which prey on other bacteria; after contact with prey, Bdellovibrio enter periplasmic space, grow and divide using host nutrients and lyse the host cell. c. Gram positive bacteria form their own  2 Phyla:  Low GC Gram Positives and  Actinobacteria   i. Gram positive bacteria (low GC): non-endospore-forming cocci and rods (Staphylococcus, Streptococcus, Sarcina, Lactobacillus); endospore-forming  bacteria:Bacillus, Clostridium, Sporosarcina, and Heliobacterium - (a photosynthetic bacterium); cell wall-less gram positive bacteria, Mycoplasma, have sterols and lipoglycans to stabilize membrane; often pathogenic.   ii. Actinobacteria: Mycobacterium - mycolic acid in its cell walls (acid-fast bacteria) often pathogens; and Streptomyces and Actinomyces,  which are filamentous soil bacteria; some species produce antibiotics. d. Spirochetes - This phylum contains gram negative, tightly coiled, motile bacteria with a unique method of motility. The flagella extend from both poles and are enclosed in an outer sheath; the protoplasmic cylinder and flagella rotate in the opposite direction as the outer sheath. This group includes free-living aquatic organisms such as Spirochaeta and a number of pathogenic genera including Treponema, Borrelia, and Leptospira. II Phylogenetic overview of Archaea   a. Crenarchaeota - mostly hyperthermophiles; also non-thermophilic marine organisms; Euryarchaeota - physiologically diverse includes extreme halophiles, extreme acidophiles, and methanogens. Autotrophy in Archaea proceeds by acetyl-CoA pathway, reductive citric acid cycle and 3-hydroxyproprionate cycle; some may have RubisCO enzymes.   b. Extreme Halophiles require high NaCl concentrations; use K+ as a compatible solute; cell wall stabilized by Na+ ions. Certain halophiles carry out light mediated ATP synthesis using bacteriorhodopsin. This protein contains retinal, a pigment that absorbs light energy and pumps a proton across the cell membrane. ATP synthesized using proton translocating ATPase. III. Photosynthesis - conversion of light energy to chemical energy by absorption of quanta of light by chlorophyll (or bacteriochlorophyll) pigments -  light-harvesting chlorophylls and reaction center (RC) chlorophylls. Photosystems contain membrane-bound electron transport systems. a. Photosynthetic membranes - allow for development of light-driven proton motive force; Thylakoid membranes in chloroplasts and cyanobacteria; Chromatophores in purple bacteria; chlorosomes in green sulfur bacteria b. Anoxygenic photosynthesis: model system - purple phototrophs (Rhodobacter). Reaction center donates e- to quinones (Type II reaction center).    i. Light harvesting complexes (antenna bacteriochlorophyll a molecules) funnel light to reaction center (RC).    ii Cyclic photophosphorylation: RC contains 3 polypeptides, 2 molecules of bacteriochlorophyll a (special pair) and two other chlorophylls plus 2 bacteriopheophytin (Bph = bacteriochlorophyll a without the magnesium) plus 2 quinones. Light energy (excitons) passed from antennae causes special pair to become photo-oxidized and to pass electron from P870 to Bph, then to intermediate quinones. Then e- enters the quinone pool within chromatophore membrane and is passed to the cytochrome bc1 complex. At this point protons are extruded and PMF is generated. The oxidized B870 in the RC is reduced when the electron from cytochrome bc1 is passed first to periplasmic cytochrome c2 which then shuttles the electron to the RC.   iii ATP synthase (F1Fo ATPase) is used to make ATP at the expense of PMF.    iv. The green sulfur bacterium Chlorobium and the gram positive phototroph Heliobacterium have photosystems with a type I reaction center. These have chlorophyll a or a modified chlorophyll a, which reduces an Fe-S center, which can pass electrons to quinone, cytochrome bc1, cytochrome c and back to the RC.    iv Autotrophy in purple bacteria. In order to fix CO2, the cell must have a sources of ATP and reducing power in the form of NADH or NADPH. To reduce NAD(P)+ to NAD(P)H for CO2 fixation, the phototroph takes electrons from photooxidation of its chlorophyll. Since the electrons that come from photosynthesis in purple bacteria are at the Eo' of quinones (~ 0 volts) energy must be consumed by reverse electron transport to force electrons against the thermodynamic gradient to reduce NAD+ to NADH. In contrast, in green sulfur bacteria and Heliobacteria, the Fe-S center can pass electrons to ferredoxin, which directly serves as electron donor for NAD(P)+. If the electron is used to reduce NAD(P)+ other sources of reducing power must be used to re-reduce the oxidized reaction center. In purple sulfur bacteria (Chromatium), H2S or thiosulfate S2O3- can be used as electron donors. Purple non-sulfur bacteria (Rhodobacter) can use H2, organic compounds, or H2S (at low concentrations) as electron donors. Green sulfur bacteria (Chlorobium) can use H2S or So as electron donors. Heliobacteria appear to be photoheterotrophs. c. Oxygenic photosynthesis: model system ? cyanobacteria and Prochloron: photosystem I and photosystem II (PS I and II).   i. Photosystem II chlorophyll P680 absorbs light quanta and ejects an e-. The P680 is immediately reduced by water releasing oxygen. The electron passes through pheophytin and bound quinones and then to cytochrome bf and plastocyanin. The latter donates e- to photosystem I.  ii. Photosystem I chlorophyll P700 absorbs light energy and is reduced enough to allow for conversion of NADP+ to NADPH via ferredoxin as an e- carrier. ATP synthesis occurs when PMF is generated by e- transport in PS II and by cyclic photophosphorylation in PS I. IV. Autotrophs are organisms that use CO2 as a carbon source. Autotrophic CO2 fixation: the Calvin cycle; Ribulose bisphosphate carboxylase (RubisCO) ? directly involved in CO2 fixation using ribulose-bis-phosphate as the substrate and producing 2 molecules of phosphoglyceric acid (PGA); PGA converted to 1,3-bisphosphoglyceric acid using ATP as the energy source; 1,3-bisphosphoglyceric acid is reduced to glyceraldehyde-3-PO4 by NADPH.  Some bacteria, such as the green sulfur bacterium Chlorobium, use the reverse citric acid cycle to fix CO2. Chloroflexus (green non-sulfur phototroph) and certain hyperthermophilic Archaea use the hydroxyproprionate pathway (not responsible for details of either reverse citric acid cycle or hydroxypropriate pathways). V. Chemolithotrophy ? the use of inorganic energy sources as electron donors to produce PMF and thus make ATP using ATP synthase. Electrons are transferred by a membrane-associated electron transport chain; often O2 is the final electron acceptor. a. Oxidation of hydrogen - Hydrogen bacteria such as Ralstonia have hydrogenase which splits H2 into protons and electrons and uses an electron transport chain with O2 as the final electron acceptor. The hydrogen bacteria can fix CO2 using the Calvin cycle. They have a cytoplasmic hydrogenase which can be used to directly produce NADH for CO2 fixation. b. Oxidation of reduced sulfur compounds ? Sulfur bacteria (ex. Thiobacillus, Beggiatoa, Thiothrix) oxidize H2S, elemental sulfur or thiosulfate; most often oxygen is the final electron acceptor, although nitrate and iron can also be used. PMF is established during the process and acidification of the medium occurs.   i. Hydrogen sulfide is oxidized to So - the electrons enter at the flavoprotein level. The So can then be oxidized to the level of sulfite SO32- and finally to sulfate SO42-.  SO32- is oxidized to sulfate by sulfite oxidase or APS reductase. The electrons reduce cytochromes during this process. The electrons are passed onto oxygen using cytochrome oxidase and generate PMF.   ii.  Some bacteria (Paracoccus) can oxidize sulfur directly to sulfate using the Sox system.